Alien civilizations rose, fell, and rose again before humans ever dreamed of visiting the stars.
The Leviathans are the oldest known intelligence. They evolved in water. Leviathans were enormous in size and reminiscent of Earth’s squid in overall design. Multiple eyes, tentacles, and a rigid armored plate system made them physically formidable, while an unexplained mental power let them dominate lesser organisms. 
Like many races to come, the Leviathans fell victim to their own creations, the synthetic Reapers, over a billion years before humanity attained space-flight. Originally mandated to preserve life at all costs, the Reapers entered an eternal cycle: allow new civilizations to evolve, grow, and spread, then harvest them to create new Reapers. The Reapers established the Mass Relay network, and the Citadel, as tools for their continual processing of organic life throughout the galaxy. 
The Leviathans were not wholly destroyed. Pockets of survivors erased all signs of their presence from the galaxy using their technology and mental influence. They created thralls from the lesser races of the time, a “Supervision Army”, that would protect their most secret hiding places. They retreated to the deepest caverns of the oceans of forgotten worlds, and brooded. They would be remembered only in myths and fables told by successor races, known by names such as “the Protodeviln”. 
Since the fall of the Leviathans, other races have fought back against the Reapers and their cyclic purges of organic life. Some were successful, others were not.
Nearly 500,000 years before human space-flight, a race of beings known as the “protoculture” dominated the galaxy. They were the first humanoids to evolve in the galaxy, and seeded it with life modeled on their own.  In time, the Reapers came for them, and they created the Zentradi army, a race of organic warriors, to defend themselves.  Though the protoculture was eventually destroyed as a society, the Zentradi were too numerous and too powerful to wipe out as well. These clone warriors left the galaxy, searching for their enemy.
Surviving members of the protoculture’s species branched out and mutated, and their seeded descendants lived and flourished. By 150,000 BCE, a human-like race of such survivors called the “Forerunners” ruled an empire of a million worlds thanks to their dominance of the Citadel and the Mass Relay network. They in turn had wrested the galaxy from their elder race, the “Precursors”, an older and different survival of the protoculture’s humanoid species. 
When the Reapers came for them, the Forerunners faced a complication: the Flood, a malignant and perverted viral form of the Precursors themselves. The Flood would assimilate any and all biomass, eventually forming vast networked intelligences and mutating whatever life it came in contact with, as a sort of biological reflection of the Reapers themselves. This, the ultimate Precursor weapon against the Reapers of their time, threatened to destroy the Forerunners in a final act of vengeance. 
The Forerunners armed and fired their own answer to the problem: the Halo Array. This devastating weapon brought an end to much sentient life across the galaxy. The Reapers attacking their civilization were wiped out, but the protoculture and its children no longer reigned.
By 68,000 BCE, a race called the Protheans emerged. Seeded by the protoculture, they had taken a different evolutionary turn. They had multiple eyes and nostrils, a thick carapace, and a unique genetic structure. They had a mental power like the Leviathans, but one for communicating and transmitting thought rather than dominating it. 
Twenty thousand years later, the Reapers came again. The Protheans had learned of the Halo Array and used its advanced design in the construction of a new weapon, called the Crucible. They were unable to construct it in time, due to the vast resources it would require. Instead, they entrusted the schematics to the future, storing them in a repository on the planet Mars, just prior to their own fall. 
The Flood was more subtle with the Protheans than with the Forerunners. The Graveminds, the guiding intelligences of the Flood, kept Flood infestations to a minimum. Undetectable infection, rather than waves of created drones, spread across the stars on Prothean starships. When the last Protheans came to Mars to bury their secrets, some samples of the infection came with them. And when a chunk of Mars was ejected toward Earth in 35,000 BCE, the Flood’s spores went too, in the form of a "black oil". 
Circa 20,000 BCE, the Supervision Army of the Leviathans was alive and well. A genetically engineered race drawn from Leviathan DNA and possessing their mental dominance power, called the “Ur-Quan”, were steadily building an invasion force they called the Hierarchy by capturing and brainwashing aliens. 
Circa 3,000 BCE, a race of “Gems”, silicon-based lifeforms who project humanoid bodies with advanced psychokinesis, come to Earth with the intent of creating more of their kind and transforming Earth into a colony world. They are thwarted by an insurgent faction more interested in preserving Earth life. The insurgents manage to drive the invasion force back home, cutting off their access to the planet, then remain for the next several millennia. 
Earth’s interaction with alien life during this time is dominated by three factions: the Reticulians, the Mor-Taxans, and the Hierarchy.
The Reticulians are a race of large-eyed, gray-skinned aliens. Their biochemistry is not based on carbon. They are cautious, cunning, and manipulative. They have been partially taken over by the Flood, and their mission is to colonize and hybridize other life-forms in preparation for the Flood’s resurgence. 
The Mor-Tax are aliens with a strongly trilateral symmetry: three arms, each with three fingers, and a three-lobed eye on a neckless head. Physically they are closer to jellyfish than mammals. They are emotionless, dispassionate, and organized in a caste structure. Their goal on Earth to secure the secrets of the Protheans. 
The Hierarchy is the cluster of races held in thrall by the Ur-Quan "masters". Each race has different strengths and weaknesses, but all work together to facilitate invasions of other planets. 
The Reticulians and the Mor-Tax were both aware of the Prothean presence in the Solar System millennia ago, and were convinced that the Protheans may have hidden something on Earth.
The Reticulians begin to scout the Earth. In 1947, a fault causes one of their stealth ships to fail and crash over Roswell, New Mexico. The United State’s armed forces immediately seize control of the wreckage and begin to analyze it. What they discover alarms the American government.
Several secret programs are initiated to deal with this new alien threat. These include Black Mesa, Project 9, and Majestic 12. Black Mesa’s charter is the study of the exotic physics and anomalous materials used to construct the Reticulians’ craft. Project 9 studies the aliens’ biology. Majestic 12 is assigned to creating cover stories, falsify or distort news reports, and otherwise manage the public relations concerning aliens.
In 1952, a group later called “the Syndicate” is organized within the State Department. The Syndicate’s initial responsibility is to coordinate the activities of the secret programs, and to collate their results. Over the next two decades, what they learn, and their relative lack of oversight, will increasingly isolate them from the national interest.
The government’s preparations pay off in 1953, when the Mor-Taxans land in Grover’s Mill, New Jersey and begin their invasion of America using giant mechanical tripods.  The Syndicate launches a biological counter-attack using a substance called the “black oil”, discovered in the Reticulian wreckage. The Mor-Taxans are captured and sealed away in steel barrels filled with the oil. Unfortunately, their unique biology began to adapt to it, even gaining some of the Flood’s ability to infect other life-forms.
By 1956, these adaptations are complete. A handful of Mor-Taxans stored on an Army base near Santa Mira, California escape their containers. They begin infiltrating human hosts, intent on conquering humanity from within. This attempt is thwarted by a few brave citizens such as Dr. Miles Bennett, who reveals his findings to the FBI.  This prompts the Bureau to open a set of files on incidents which could be due to alien action, dubbed the “X-Files”.
Elsewhere in the world, other governments are secretly preparing for the alien threat, which they became aware of through spies in the American government. A secret group called the Global Alliance is put together to keep the existence of aliens secret, and to hunt aliens who interfered with humanity.  It is joined by luminaries such as Professor Bernard Quatermass, whose British Rocket Group analyzes an alien device in 1958, found buried under London, and finds evidence of prehistoric tampering with human beings in an attempt to give them psychic powers. 
The Reticulians, meanwhile, send a second expedition back to Earth. They manage to learn about the Syndicate’s existence and open a dialogue with key members. The Syndicate is shown enough of the gray aliens’ capabilities to become convinced that Earth could not survive a concerted alien invasion. By 1973, the Syndicate is operating independently of the State Department’s oversight, forming a shadow government that prepared to facilitate, rather than oppose, the invasion.
In 1982, a Norwegian Antarctic base sends out personnel who get too close to a Reticulian secret base buried under the ice. It is destroyed by a shapeshifting creature, possibly a sample of the Flood, who then almost completely destroys a nearby American outpost. 
In 1987, American commandos on a mission to rescue a VIP from a jungle prison encounter an unknown alien life form, which apparently takes pleasure in stalking them. 
In 1988, a terrorist action on an Army base manages to unseal several Mor-Taxans. They promptly take over the terrorists’ bodies and resumed their invasion plans. A small group consisting of Harrison Blackwood, Colonel Paul Ironhorse, computer expert Norton Drake, Dr. Suzanne McCullough, and her daughter Debi, worked to uncover, understand, and oppose the Mor-Taxans’ actions. 
Thanks to the work of the Blackwood Project, a pair of specially treated sunglasses is produced that will reveal human beings occupied or controlled by Mor-Taxans to the wearer. The team distributes these to every location where they’ve charted the aliens’ activity. One of the recipients of these sunglasses, an itinerant blue-collar worker, is shocked by what he sees. He goes on the run as the aliens discover he can see them, eventually taking a hostage and being betrayed. He manages to destroy a crucial transmitter used by the Mor-Taxans to transmit their hypnotic influence throughout Los Angeles. 
A city-wide panic is barely averted by Majestic 12, working with the Reticulians, but the revelation of the Mor-Taxans allows Majestic and the Syndicate to complete Blackwood’s mission and wipe the aliens out completely.
FBI special agent Dana Scully is assigned to long-time X-Files researcher Fox Mulder in 1994. Together, the pair spend the next several years researching mysterious cases, including the prior alien incursions.  Some of their information comes from abductee claims made by individuals such as Travis Walton, who reported being taken to an alien spacecraft and having horrific experiments performed on him. 
In 1995, Mulder and Scully investigate an effort by the Syndicate to create human-Reticulian hybrids, who will help facilitate the aliens’ takeover of Earth. One of these, created by Project 9, is dubbed “Sil”. She escapes her holding facility and is driven by instinct to attempt to mate with human beings and reproduce. She is eventually killed by the team assigned to track her, including Dr. Stephen Arden, Dr. Laura Baker, Dan Smithson, and Preston Lennox. 
The Global Alliance has managed to deal with isolated alien disturbances - the result of other species’ interest in the Reticulian and Mor-Taxan presence on Earth - but are unable to infiltrate or interfere with these races’ activities.
As of 1997, UFO sightings have been increasing steadily, and the Global Alliance’s best intelligence shows “something big” coming soon, thanks to an analysis of signals by astronomer Zane Zaminski.  In 1998, they invite members of the Blackwood Project, the Project 9 tracking team, selected FBI special agents, and other individuals to join a new organization. Their charter remains the same: investigate, contain, or eliminate alien threats. This new organization is known as X-COM and will work semi-openly with the government. 
The Hierarchy begins its invasion of Earth with the first of three waves. This wave, led by the Gua species, arrives in 1997. The Gua don’t physically exist on Earth; instead, they clone “husks” from human DNA, implanting them with alien tech, and transfer their consciousness into the husks. They begin experimenting with humans to determine their vulnerabilities, but also to probe for Prothean secrets or evidence of Flood contamination. 
Reformed thief Cade Foster, one of the Gua test subjects, escapes confinement. He is framed for the murder of his wife - really a Gua husk - and goes on the run. Elsewhere, Gua experiments on high school populations are disrupted by unlikely alliances between different cliques of students. 
Cade Foster manages to get in contact with X-COM and inform them of the existence of the Gua. Mulder and Scully finally learn the truth after pursuing the Foster case themselves. Following further leads, the two agents independently uncover a Reticulian spacecraft in Antarctica. The Reticulians, now knowing the Hierarchy is coming, launch their spacecraft, taking with it numerous hybrid experiments and aliens, and abandon the Earth. 
The Gua abandon their efforts at infiltration once they have been discovered, and send out a call to the Hierarchy. In 1999, the Second Wave arrives. The Hierarchy’s fleet of massive starships - the largest on par with Earth’s moon - enters Earth’s orbit. The ships attack major population centers in a devastating bombardment.
The Syndicate, abandoned by their Reticulian allies, takes a gamble and hands over the alien data it has been collecting since 1947. Based on this data, the President authorizes a nuclear strike, but it is ineffective due to the Hierarchy ships’ force fields.
With the help of Guan traitors sympathetic to the human cause, the X-COM team at Area 51 is able to supply access codes that will unlock the shields of the motherships. David Levinson and Captain Steven Hiller are instrumental in delivering a nuclear device to the fleet mothership in one of the Hierarchy’s own fighter craft, using these access codes to bypass the shields. The destruction of the mothership, and other ships in the fleet, ends the immediate threat of Earth’s destruction. 
Several of the Hierarchy’s other alien races have already landed. X-COM is mobilized to deal with these forces. One minor species, for whom water is acidic, is apparently sent to Earth as a joke by the Ur-Quan masters, who also used their psychic powers to compel human beings to create crop circles as signals for them to follow. 
One of the damaged Hierarchy ships soft-lands on South Ataria island.Scientists begin an immediate program to salvage and repair it, dubbing it the “Super Dimension Fortress”, or SDF. 
In 2003, a member of the Syndicate known as the “G-Man” obtains a sample of the SDF’s space-fold engine. This sample, known alternately as fold quartz or Xen crystal, allows faster-than-light travel through an interstitial space.
The G-Man brings the sample to Black Mesa for analysis by the Anomalous Materials laboratory. This results in a resonance cascade which opens dimensional portals from Earth to another place and critically damaging much of Black Mesa’s infrastructure. Many personnel are killed or trapped. Only one scientist, Dr. Gordon Freeman, is able to escape the chaos.
As a result of the resonance cascade, an extradimensional faction of aliens known as the Nihilanth send their foot soldiers - headcrabs, vortigaunts, and other creatures - through dimensional portals opened by the cascade. 
X-COM’s HECU (Hazardous Environment Combat Unit) is dispatched to Black Mesa to contain the situation and deal with the alien presence. Thanks to the G-Man, they are erroneously informed that the scientists at Black Mesa were deliberately attempting to create a dimensional breach and facilitate an invasion of Earth. The HECU is unprepared for the outpouring of creatures from the portals, and only Corporal Adrian Shephard is the only survivor of his unit. He witnesses Dr. Freeman crossing the dimensional barrier in the Lambda Complex of Black Mesa.
Dr. Freeman enters the “border world” of Xen, fighting the Nihilanth’s forces using military weaponry supplied by the Lambda team. He is able to kill the master Nihilanth whose energies were maintaining the portal storm, closing the portals and preventing an immediate invasion of Earth.
Black Mesa itself is destroyed by a nuclear bomb set by the G-Man. Both Dr. Freeman and Corporal Shephard are abducted by the G-Man, and no trace of them can be found.
X-COM speculates that the Syndicate was attempting to negotiate with the Nihilanth through the G-Man, hoping to use them as a counter to the Hierarchy’s invasion. The resonance cascade was a way to allow the extradimensional aliens’ forces to enter Earth, but when the Syndicate found that the Nihilanth had no intention of cooperating, they destroyed the facility.
By 2009, the world is actively preparing for another attack. However, X-COM was built for counter-insurgency and special operations, rather than all-out warfare. Their technologies, data, and training are now integrated into a larger, international standing army. The result is UN Spacy - the United Nations Aerospace navy and marine force.
Survivors of the earlier waves of invasion are debriefed using hypnosis, and their stories are studied and correlated by government psychologists in the hope that useful intelligence will emerge. Many of their stories include mention of certain animals or distinct odors. 
The SDF is ready to launch after a decade of work. On launch day, the alien ship’s sensors register a space-fold. According to the databanks of the SDF’s computers, the newcomers are known as the Zentradi - the ancient cloned warriors of the protoculture - and have come in search of their enemies, the Hierarchy. Despite its rebuild by humans, the SDF is still considered an enemy.
To lead these hostile newcomers away from Earth, the SDF tries to execute its own space-fold to the far side of the moon. Instead, the ship and a complement of 70,000 civilians - the town that had sprung up on South Ataria island to work on the rebuild effort - travel instantly through space to the planet Pluto. Fortunately, the Zentradi followed.
For the next two years, the SDF, dubbed “Macross” by its inhabitants, successfully fended off Zentradi attacks. To combat the 60-foot Zentradi clone soldiers, they use alien “overtechnology” to create advanced aerospace fighter jets that can transform into humanoid robots. Initially they are forbidden from returning to Earth and bringing the Zentradi threat back to humanity’s homeworld.
In 2011, the Third Wave of the Hierarchy comes to Earth. Aliens in biomechanical suits attack major cities like Los Angeles, and encounter opposition from UN Spacy’s marine forces.  Elsewhere, other aliens use hypnotic blue beams to hypnotize and teleport humans away for forced conversion into biomechanical components of the alien war machine.  Mysterious energy-eating aliens land in Moscow and begin disintegrating the populace, with a few survivors managing to evacuate via submarine.  Navies engage the aliens in the open ocean, notably the USS John Paul Jones which manages to destroy an alien flagship.  A few unintelligent but vicious alien parasites land in places like Brixton, to be fended off by local street gangs. 
The most powerful aliens in the Third Wave are called the “mimics”, monstrous and polymorphous aliens with an uncanny ability to anticipate human battle strategy. By this time, the “mecha” technology used by the SDF has been miniaturized to such an extent that rank-and-file soldiers can be equipped with armed exoskeletons, or “Jackets”. Using these Jackets, and a mysterious property of the mimic blood that allows the affected person to mentally travel backwards in time, soldiers William Cage and Rita Vrataski are able to locate the master “Omega” mimic and destroy it. With the source of their time-winding powers destroyed, the tide is turned against the mimics. 
If the Zentradi are the enemies of the invading army, commanders reason, maybe they will aid humans in fighting off the invasion. The SDF is finally permitted to return to a war-torn Earth in 2012, and the Zentradi follow.
On December 21st, the Zentradi devastate the Earth’s surface in a massive attack, which wipes out the majority of the Third Wave’s remaining forces but also does considerable damage to human infrastructure and takes many human lives.
The Macross crew have discovered something about their Zentradi enemies: they have no culture of their own, and they revere the protoculture. Using common human emotions and emotional gestures - music, kissing, and expressions of love - they cause many Zentradi soldiers to become sympathetic to their cause. A few friendly commanders realize that humanity is itself descended from the protoculture and switch sides. Together, they create a plan to stop the larger Zentradi armada from completely eradicating Earth. Using this plan, the Macross and the allied Zentradi manage to wipe out the rest of the armada.
Despite the peace, humanity is unwilling to fully forgive or accept the Zentradi for their genocidal actions, despite the good intentions of the turncoat giants. The Zentradi ask for human volunteers to come with them and teach them culture, and with these volunteers, they fold out of the solar system.
Many of the Hierarchy’s ships have crash-landed on Earth but are somewhat intact. In 2013, the forces of the Nihilanth on the border world of Xen use one of these ship’s fold engines to open a dimensional breach in the Pacific Ocean. They send gigantic biologically engineered monsters, called “kaiju” by the humans, through this breach to attack a war-ravaged and exhausted humanity.  The first emerge of a kaiju is later known as “K-Day”, and is documented by citizen journalists such as Hudson Platt. 
By 2015, conventional military forces have proven thoroughly ineffective against kaiju incursions. This “Small War” causes military planners to rethink their approach. They turn to the SDF and the alien overtechnology, taking their robotic creations as a model. They build gigantic non-transformable robots, called “Jaegers”, operated by two or more pilots operating in a neural handshake with each other. The defense contractor Aperture Science provides its expertise with artificial intelligence to control the Jaegers, and its study of the space-fold engine and related “portal” technology is vital in understanding how to close the breach.
The Jaegers prove effective, temporarily. However, the rate of kaiju incursions steadily increases, to the point that they are destroying Jaegers faster than they can be built. In 2025, only a handful of Jaegers are left, under the command of Marshal Stacker Pentecost. He assembles a team of pilots for a last-ditch effort to close the breach. Pilots Raleigh Becket and Mako Mori are able to penetrate the breach and detonate the Jaeger “Gipsy Danger”'s nuclear engine in the middle of Xen. The two pilots return through the breach to safety, but Marshal Pentecost and his co-pilot Chuck Hansen are lost operating “Striker Eureka” to cover their run.
The SDF’s misaimed fold, plus the potential of another invasion force from alternate dimensions, leads governments to seal away use of the space-fold engine.
In 2041, it is discovered that the Nihilanth sent through numerous smaller forces in addition to the kaiju, and that these have been building up military bases under the ocean. UN Spacy comes under attack, but defeats them within a few years. 
2045 marks the centennial of the second World War and the end of alien hostilities on Earth. Mankind, shattered, exhausted, but alive, makes a collective decision: It’s time to take the fight to the stars.
The next seven decades see humanity spreading throughout the solar system and preparing itself to meet the next visiting race.
By 2050, colonization of the solar system proceeds in earnest. Lunar bases and orbiting factories are set up as launch pads for the other planets. Research begins on faster-than-light technology that doesn’t depend on the space-fold drive.
The American STARCOM (Star Command) program is formed in 2055 as a military-scientific organization, separate from UN Spacy, and operating in space and using combined arms and advanced technology. They experiment with a limited version of the space-fold engine, called "transtar". Their biggest enemy is not an alien force, but a mad scientist who calls himself “Emperor Dark”, and makes use of alien technology provided by an unidentified species. 
In 2059, a mysterious constellation of fold portals opens over Earth, and an insect-like alien species emerges for a few minutes. They disappear as quickly as they came. 
Armstrong Outpost becomes UN Spacy’s biggest military base on the Moon, centered on the Shackleton Crater. It is inaugurated in 2069, a century after man first went to the Moon, and becomes the capital of Luna shortly thereafter.
In 2070, billionaire Victor Manswell, CEO of the Union Aerospace Corporation, becomes frustrated with the pace of human exploration. He begins preparing his own expedition. UAC contracts with UN Spacy to research space-fold technology on an isolated research station on the Martian moon of Phobos.
Teleportation experiments between Phobos and Deimos initially appear promising. A disastrous accident overtakes the Phobos base in 2072, and forces brought through the space fold kill or mutate almost everyone in the facility. The only survivor is an anonymous UN Spacy marine, who fights his way through the hordes of altered creatures to shut down the experiment. 
Despite this setback, the Manswell Expedition departs in 2075, bound for the Alpha Centauri system. They will not be not heard from for over a century. Speculation at the time that the space fold drives malfunctioned or went off course renews determination not to use the technology until it is better understood. 
In 2080, the United Nations institutes organizational changes to UN Spacy. The Manswell Expedition exposed a weakness in how the military interacted with private corporations. The new organization, modeled on STARCOM’s success and given the similar-sounding name “Star Control”, will not only defend the Earth, but the solar colonies, and will be more self-contained and less dependent on private contractors.
Decades prior, scientist Hsien Ho led a project to create "androsynths", a synthetic humanoid that would aid mankind in rebuilding a shattered planet. In 2085, an androsynth rebellion is put down, but numerous androsynths are unaccounted for, and it is widely believed that they folded out of the solar system. 
In 2093, the Weyland Corporation follows Manswell’s example, and secretly sends the science ship “Prometheus” to distant world LV-223. Aboard is corporate founder Peter Weyland, the androsynth “David 8”, and a complement of scientists including Dr. Ellie M. Shaw. Their goal is to discover the source of the “black oil” and perhaps trace the origins of life on Earth. LV-223 is one of three moons located in Zeta Reticuli, the home constellation of the Reticulians that dealt with the Syndicate. The expedition is also never heard from again. 
In 2103, the European Space Agency’s Lowell City becomes the first permanent human settlement on Mars. Located in Eos Chasma, the site seems ideal at first. However, satellites and local observations in the area give unusual readings, and strange phenomena earn the area a reputation for being “haunted”. 
Inspired by the old stories of the Global Alliance and their “Roswell conspiracies”, the son of Lowell City’s Mayor Jones assembles a few friends, and a caniform androsynth companion, to investigate haunting rumors in the hope of discovering new forms of alien life. 
In 2112, Ceres Base is constructed by Star Control. This marks the largest space-borne military outpost, and the current extent of humanity’s colonization.
During this era, humanity becomes an active participant in galactic politics. Distrustful of aliens due to the repeated invasions of Earth and the rest of the solar system, most of man’s interactions with other races proceed from a martial posture.
In 2115, the Chenjesu arrive in the solar system. They are a race of silicon, crystalline beings, with advanced technology and high intelligence. They are aware of the Hierarchy’s invasion of Earth in 1999, and offer humanity a place in the “Alliance of Free Stars”, which intends to combat the Hierarchy and their Ur-Quan masters. 
After a few weeks of deliberation, and system-wide voting, humans join the Alliance. They join the Chenjesu, the Mmrnmhrm (mechanical beings from the Virginis constellation), the Yehat (a pterodactyl-like race), the Shofixti (marsupials uplifted by the Yehat), and the Syreen (a blue-skinned race of psychic humans).
The Nostromo, a cargo spaceship carrying raw materials for the war effort, disappears after investigating a signal on planet LV-426.  Hierarchy interference is thought to be responsible.
By 2126 the Alliance is ready for war. Humans contribute material and labor, while the other races provide technological assistance. The next eight years is a melee of between the Alliance and the Hierarchy. Many battles are won, and many are lost. Ultimately, the Hierarchy is driven out of the spiral arm. The cost is high: the Alliance has disintegrated. Each race has lost too much, and lacks the political will to continue participating. Humanity is left to fend for itself.
The construction of Gagarin Station begins in 2143. This facility, located beyond Pluto’s orbit, is the next attempt to master space-fold technology and solve the mysterious repeat disappearances of fold drives and sometimes the ships carrying them… After five years, the researchers pinpoint the cause of the interference: emanations from Mars, and Charon, Pluto’s largest moon - in reality a gigantic apparatus called a “mass relay”, a gateway to the stars.
Researchers uncover the Prothean cache on the Red Planet, and begin to unravel the secrets of element zero, or “eezo”. A year later, the Charon Mass Relay is activated for the first time. Extrasolar colonization is now in man’s hands.
That year, 2149, marks the signing of the Systems Alliance charter. While the United Nations represents all nations on Earth, the Systems Alliance will represent all of Earth’s colonies throughout the galaxies.
The mass relays open the door to human colonization of nearby systems. The Delta Pavonis Foundation begins settlement of the first extra-solar colony, the planet Demeter. Later that year, other colonies are founded on Eden Prime and Terra Nova.
Humanity meets a new aggressor in 2157 in the form of the Turians, who attack them for activating a dormant mass relay. The Citadel Council, of which the Turians are members but which the humans know nothing about, has ruled such actions illegal. The conflict is relatively bloodless - only a few hundred lives are lost on both sides. The Council quickly negotiates a cease-fire once they learn about the situation.
In 2160, the Systems Alliance Parliament is created to give a voice to the new colonies. Three years later, the United Nations Space Command replaces Star Control as the premier military-scientific organization responsible for protecting Earth. The UNSC will report to the Systems Alliance, rather than the United Nations. Privately, it is widely believed that structure and leadership of Star Control were to blame for humanity’s warlike response to the Turians, and that it is time for new blood.
In 2165, humanity is granted an embassy on the Citadel - a massive, high-tech space station that acts as the hub of civilization in the galactic region. Though mankind has a reputation for aggression and fractiousness, the leading voices on the Citadel Council - the Asari, the Salarians, and the Turians - recognize that Earth’s history of hostile alien contact is responsible for this attitude.
In 2176, a group of police assigned to escort a dangerous prisoner find out that the inhabitants of a mining town on Mars have been killed or have disappeared. The cause is a series of psychic emanations from the Prothean cache, reacting to the imminent approach of the Reapers, causing local humans to become “possessed”, ritually scarify themselves, and attack anyone not also possessed. 
In 2179, Warrant Officer Ellen Ripley of the Nostromo is recovered in an escape pod, and briefed by the Weyland-Yutani corporation. The colonization of planet LV-426 ran into a problem and the company wants her assistance. UNSC marines are dispatched to investigate, with Ripley acting as a special advisor. Together they discover an infestation of Flood xenomorphs. The survivors destroy the colony, and the infestation, using the colony’s nuclear reactor by causing it to go critical. Only Ripley, Corporal Dwayne Hicks, and a surviving colonist named Newt survive the incident. 
The most momentous events of this era begins in 2183 with the Eden Prime War. The Geth, a synthetic race created by the Quarians, have secretly allied with the Reaper Sovereign, in preparation for the Reapers’ repeated conquest and destruction of organic life in the galaxy. One member of the Systems Alliance, Commander Shepard, is instrumental in relaying information about the Reapers to the Citadel Council. 
In 2185, Shepard is revived by a human-supremacist terrorist organization called Cerberus. The Commander investigates disappearances on human colonies, uncovering the actions of a race called the Collectors. In reality, these are indoctrinated remnants of the long-lost Protheans, created by the Reapers as tools. 
The Reaper action in the galaxy comes to a head in 2186, when they invade the galaxy en masse. Shepard discovers the plans for the long-lost Prothean super-weapon, the Crucible, and is responsible for driving a galaxy-wide war effort to build up the resources needed to construct and fire it.
As the Reapers approach and besiege Earth, Shepard activates the Crucible. It fires, destroying the Reapers, but also crippling or damaging the mass relay network throughout the galaxy. 
With the mass relay network shut down, Earth is cut off from the rest of the galaxy. Now free of mass-effect interference, space fold technology works without complication.
In 2199, an alien race called the Gamilas begin unleashing radioactive bombs, delivered via meteorite, across the Earth’s surface. Humans retreat into underground shelters for protection, but most have been affected by the radioactivity and have limited lifespans. The Gamilas follow up their bombardment with a powerful space fleet, which does considerable damage to the war-ravaged Systems Alliance navy.
Earth receives a message from the planet Iscandar, in the direction of the Large Magellanic Cloud. Their leader, Queen Starsha, offers humanitarian aid, including a technology that will repair DNA damage done by the Gamilas. Cut off from the surface by the radiation and meteoric bombardment, human engineers build a new ship, the Yamato, using the only materials they have easy access to - the underwater wrecks of battleships and starships. They manage to equip it with a reaction weapon called a “wave motion gun”, similar to the SDF’s main gun, and a modified version of the space-fold engine.
The Yamato completes its one-year journey to Iscandar, eventually defeating the Gamilas invasion forces and learning their secret: their own planet is dying, and they had hoped to use Earth as a new world. 
Expeditions to Epsilon Eridani uncover several alien races in the region. In 2245, the commander of the Earth vessel Prometheus initiates hostilities with one such advanced race, the Minbari. The Minbari efficiently exterminate the human military forces they encounter. To everyone’s surprise, the Minbari surrender immediately on the verge of conquering Earth, at the Battle of the Line in 2247. The Minbari secretly identify the humans as members of the “protoculture”, from which they also descend, and find both a biological and psychic affinity between the two races. Their religious law forbids conflict with their own kin.
Between 2252 and 2262, a succession of five space stations are established in Epsilon Eridani space by the Earth forces. Recognizing the value the Citadel provided as a place for diplomacy and commerce, mankind inaugurates their own version of the concept, the "Babylon" station. Babylon 5 welcomes ambassadors from the rival Centauri and Narn races, as well as many other aliens. 
In 2259, Earth is attacked by meteorites again, this time sent by a race of genetically modified insects dubbed the “Bugs”. The UNSC speculates that the Bugs were created from the rachni and have been observing the Earth-Gamilas conflict to learn about Terran weaknesses. The armed forces mobilize to strike back against the Bugs, tracking them to their home base on the planet Klendathu. 
By 2261, Earth - thanks to the attacks from the Bugs - has become increasingly militarized and fascistic. The leadership limits voting and many other civil rights to those who will serve in the armed forces, institutes rationing, and cracks down on dissent. In response, several human colonies, and Babylon 5 itself, secede from the Systems Alliance and eventually invade Earth to liberate it from the despotic regime of President Clark.
By 2291, advances in space-fold technology lead to the "slipspace" drive. Similar to frequency-hopping radios used by the military, ships could “slip” through fold waves, effectively disguising their point of origin and bypassing many of the dangers of folding space.
More and more, strategic planners agreed that aliens knowing the location of Earth was itself a risk. Increasingly stringent methods of protecting Earth’s location were instituted, culminating in the “Cole protocol” of 2540 that meant a ship’s captain would blow his ship up and suicide rather than let aliens seize control of the ship’s navigational computers.
In 2321, the ORION program is green-lit. Compared to many alien races, humans are physically lacking. Since many alien races have been found to be genetically compatible, work gets underway to engineer a trans-human soldier, using the best of mankind’s genes and the most useful alien genes available.
In 2362, the planet Reach in the Epsilon Eridani system is colonized. It becomes the new center for the UNSC’s military and is fortified against any conventional attack. The rationale is that if Earth falls, humanity’s military might shouldn’t be compromised as well. Reach becomes the home of the SPARTAN-II program, the successor of ORION, using genetic material from human heroes such as Commander Shepard as the template for a batch of super-soldiers.
Military technology has gradually learned from the ancient Zentradi warriors’ doctrine: simple, rugged, and predictable often beats high-tech. Soldiers can’t be mass-produced, but equipment can. Slug-throwers and mass-driven weapons continue to be used despite an understanding of high-energy and exotic physics.
In 2525, humanity is first attacked by a theocratic alliance of aliens known as the Covenant. Led by a pact between the San 'Shyuum and Sangheili, the Covenant worshipped the Forerunners and other ancient aliens as gods, and the destruction of the mass relay network by humanity is effectively heresy.
The next twenty-eight years sees a continual state of war between the UNSC and the Covenant. In 2552, the Covenant come to Reach and eventually prevail over the human military forces protecting it. 
At the same time, a human ship called the Pillar of Autumn comes across one Halo, now infected by the Flood and under the control of the Covenant. They prevent the firing of the Halo (an event which would wipe out much of the organic life in the galaxy, as had happened once before). 
The next six years is a whirlwind of warfare. The UNSC struggles to protect humankind against the Covenant, while dealing with the resurgence of the Flood, the activation of Forerunner artifacts, and an eventual invasion of Earth. The Battle of Installation 00 marked the effective end of the Covenant, as it was torn apart by internal schisms, the assassination of key leaders, and the stresses of war. 
In 2629, humans encounter a race of hostile feline aliens called the Kilrathi. From then until 2671, sporadic fighting between the two species keeps humanity on a war footing. 
In 2633, alien allies of the Kilrathi, dubbed the “Red Falcon”, manage to land on Earth and set up a base. Engineered super-soldiers Bill Rizer and Lance Bean are dispatched to deal with the infiltration, and manage to destroy the base. 
Centuries of fighting off extraterrestrial invaders, of leading and following, has matured humanity. In the decades following the war with the Kilrathi, human starships spread throughout the stars. From Epsilon Eridani to Council space, Earth’s war vessels come with seasoned warriors, simple but powerful weapons, and a message:
“We are not your leaders, nor your slaves. We are your Shepherds.”
Humans have in effect become the new Zentradi, protecting the children of the protoculture and their allies. Any race that needs assistance can petition them for protection. Unlike the Zentradi, humanity also has its own culture and emotional fulfillment. They will want for nothing.
There may always be war in the galaxy, but peace has never been closer.