I've been kicking this idea around in my head for a while, so I decided that now's the time to get it out.

This story will use X-COM Enemy Within as a backstory, not Terror from the Deep, so no Aquatoids, Sonic Weapons (for now) or T'Leth. Obviously, this story will also not follow the "canonical ending" that leads into X-COM 2.

At the moment, I am not sure if I want to implement Mutons into Shepard's squad. If you have any ideas on that, please tell me in the reviews. No guarantees, but if I draw inspiration, you'll get credits...and a cookie!

Final Note: I do not own X-COM or Mass Effect.

Prologue

2017

The destruction of the 20-kilometer long Temple Ship halted the alien invasion in its tracks. The backlash from the death of its commander overwhelmed the rest of its kind, resulting in the psionic immolation of every last ethereal on the planet. This was later discovered to be a result of the massive psionic communications network employed by the alien forces. Unfortunately for Earth, that meant the loss of control over their subordinate races and the subsequent crash landings of all their craft in the skies.

By the time the world militaries scrambled to the crash sites all around the globe, the craft had all been abandoned, leading to a massive effort to track down and contain every last alien. In order to better coordinate recovery and salvage efforts, X-COM was semi-revealed to the world under the guise of the UN establishing a crisis management team. Using disguised laser weapons and retrofitted interceptors, teams of now highly-experienced operatives moved in to capture or eliminate the disorganized alien invaders. To take precautions against the possible continued existence of the rogue organization EXALT, the alien ships were stripped of their Elerium and Meld technology by X-COM before any other individuals were allowed into the area.

Several Chrysallid outbreaks occur within the Amazon Rainforest, and tensions rise across the world when X-COM's cover organization orders a massive military bombardment of the rain forest. Environmentalists across the world decry this response, with several extremists persisting in protest in spite of "new discovery" of the effects of a Chrysallid infestation. Nevertheless, the world militaries prepare for the worst and begin training entire cities in quarantine protocols. The US and Canadian military send a rapid response force to monitor South America as well as coordinate relief efforts for the civilian populations. Soon afterward, sections of Africa are also declared infested and cordoned off by European Union Emergency Response Forces.

Finally having untouched and fully-functioning alien computer banks, X-COM begins the long and arduous process of decrypting and deciphering the alien archives. They are aided by surprisingly cooperative Sectoid Commanders and their lesser brethren, who in the absence of Ethereal domination revert to mindlessly maintaining technology.

2018

X-COM's efforts in extracting information lead to the conception of an anti-Chrysallid virus. Further development and eventual deployment takes six more years, during which several more large areas of the world have been quarantined. To the relief of the world, it is learned that there is a certain level of bio-mass required to sustain a Chrysallid infestation, and that Chrysallids possess a natural aversion to water. Large "water-breaks" are subsequently constructed around each quarantined area. Several Chrysallid specimens are captured by deep strike MEC teams for experimentation and testing.

Reports begin coming in of individuals developing strange abilities post-invasion. Completely without X-COM input, the authorities of the world take to apprehending and isolating them from the rest of the population before requesting further direction. Due to this effort and a later cover story, the civilian populace is kept ignorant of the existence of Psionics. X-COM determines that this new mass development results from innate sensitivity coupled with the backlash from the death of the Ethereals. The newly-discovered Psionic individuals are hidden away, and later form the progenitor of the Systems Alliance Military.

X-COM discovers a faint Psionic signature at the site of an explosion, later revealed to be the Volunteer, Colonel Marcus Summers. Severely wounded and comatose, he is immediately repatriated by his comrades.

2025

With the information gleaned from the alien archives, humanity has made many enormous jumps in medical technology. Meld is selectively doled out by X-COM to carefully vetted and briefed institutions, who use it to develop transplant procedures, cures for auto-immune and neurological diseases and life-extension.

Also dredged from the alien archives is a translation suite for the various races. Proper communications open up with the Mutons and Cyberdiscs. While the mutons have little to add to what is known about them, the Cyberdiscs are discovered to be an example of naturally evolved AI, developing from protocells into silicate-based insectoid life, and then augmented by the Ethereals with an organo-metallic carapace and integrated weapons systems. With communication comes a level of understanding. The Cyberdiscs were part of the Ethereal forces out of gratitude, but had not signed up for the campaign of forced uplift or assimilation.

The Cyberdiscs also reveal that the Mutons are bioengineered soldiers with little independent thought. The failures are remade into Floaters, the low-quality standard troops are simply cloned templates, and the Muton Elites are simply limited successes at creating an autonomous warrior race. This revelation chills X-COM as they realize how lucky they were not to face an army of much smarter and better conditioned Muton Elites.

Communication with the Muton Elites or True Mutons leads to their race understanding how they had been used by their creators, and how they are now free to choose their own path as a species, within reason of course. Tensions lessen around the containment camps once it's clear that the two races are not innately hostile.

The Thin Men are coaxed into working with X-COM's research teams and providing new information, having little alternative and lacking direction from a Psionic Overseer.

2029

X-COM manages to recreate the Drive technology used by the Ethereal forces with the aid of the Sectoids, Cyberdiscs and Thin Men. A large "lifter' platform is created with these drives to bring large amounts of material and equipment into orbit around Earth, and eventually deposited at Lagrange Point 2. Plans are made to transform this mass into Earth's first spaceyard. It eventually becomes the Lagrange Construction Center.

In the interest of heading off international tensions and jealousy, X-COM is fully revealed as the organization responsible for beating back the Ethereal Invasion. This is coupled with a clarion call for international unity, and results in the ratification of the Earth Alliance, subsequently to be renamed into the Systems Alliance during the Humanity's age of interstellar colonization. The unification results in the Council being elevated to a planetary government position, and in X-COM becoming a space-faring military force. The LCC begins construction of the first Human warship Enterprise, named by popular vote and planned out as a carrier.

Colonel Marcus Summers reawakens to the sight of an older trio of Central Officer Bradford and Doctors Shen and Vahlen. With X-COM's public reveal, Colonel Summers is hauled out and celebrated as the hero that Humanity needed. Marcus Summers is subsequently promoted to General, and placed in command of X-COM's military forces "whenever you decide to come back." It's an offer taken after receiving MEC augmentation to replace his lost right arm and left eye.

Quarantined Areas begin full-scale deployment of the anti-Chrysallid virus after finishing preliminary testing and small-scale deployment.

Mass-Production of laser weaponry for the Alliance military begins. Plasma and the Fusion lance weaponry are kept hidden away to serve as the "ace in the hole" for X-COM's special unit. SHIV weapons and upgrades are redesigned to be applied to Main Battle Tanks. X-COM's carapace armor becomes standard issue, and undergoes continuous refinement in the future decades. The Vahlenite Armor used in the Titan system is restricted for X-COM's elite forces.

2040

Alliance Surveyors discover a crashed yet astonishingly intact Temple Ship computer archive on the Moon. The great mystery prior to opening it is figuring out how it survived. Among other things, the most important discoveries the Alliance finds is a method of mass producing Elerium, the complete plans for the Temple Ship's Wormhole drive as well as astronavigational data. A retiring Officer Bradford calls it "the biggest and luckiest gift horse humanity has ever seen."

X-COM establishes the Jovian Training and Production Center, with a much larger set of shipyards and a Zero-G infantry combat training center for its elite forces. The center also functions as a testing facility for prototype technology. The Alliance First Fleet, while still unfinished, sees simulated action in war game scenarios and also provides lifting capacity for the construction efforts. As a result of the wargames, priority is placed on constructing heavy fighters with long-ranged weaponry and increased power generation over building large non-carrier capital ships.

Civilian colonization of the Moon, or Luna, begins. Surveyor teams are also sent to Mars to plan out future development plans.

2054

The Alliance has completed retrofitting of the First Fleet with Wormhole drives, and sends out the freshly constructed Second Fleet to the Alpha Centauri system, thus beginning humanity's age of interstellar colonization.

The Muton race and a newly born hive of Cyberdiscs depart with the Second Fleet and a bioengineering team, hoping to find a home for the True Mutons and remove the defects in the majority. Pre-departure testing with Meld has shown promising results.

Life extension medical science has become mainstream, if somewhat limited in the expected scale. Doctor Shen opts to retire and die peacefully as a natural unaltered human being. Doctor Vahlen and General Summers choose to stay on as X-COM personnel.

X-COM discovers the existence of a theoretical Thermal Superconductor, a highly durable substance that even the Ethereals couldn't produce.

2072

In gratitude for Humanity's aid, the perfected Muton race applies to become part of the System Alliance. After two months of public debate, the Alliance accepts. It is noted by various think tanks that this decision is less due to altruism than pragmatism: humanity requires all the strength it can muster in order to deal with a potential second incursion by the Ethereals, or any other hostile races. For similar reasons, the Cyberdiscs, or Cydonians (the original hive primarily resides in the Cydonia Research Station on Mars) have been accepted. Regardless of the motives, this agreement marks the reconciliation of humans with the thralls of the Ethereals.

Earth has been mostly rebuilt, and the human population has surpassed the pre-invasion numbers. In a bid to relieve pressure on the still-recovering ecosystem of the planet, the Alliance makes plans for colonizing the nearest habitable systems. Questions arise as to the security of the colony worlds, with X-COM declaring that the colonies will be guarded by individual planetary militias armed with laser cannons. Each colony would also have a Hyperwave relay to call for help when the militia is insufficient. Plasma weapons, fusion lances, and true military armament would remain restricted. A public outcry erupts over this proposal, though it is stifled once world leaders remind the population of how X-COM turned enemy technology against the invaders.

The Superconductor production plant and shipyard is completed and placed deep within the Oort Cloud, near the protoplanet Sedna. The facility is guarded by the Third Fleet, and heavily automated to prevent information leaks. Security around this station is the highest in the Alliance. Plans are formulated for a mobile command station for X-COM to be constructed at the station.

2100

The Fifth Fleet of the Alliance begins construction. The total number of large ships produced by Alliance shipyards crosses the thousand mark.

The Alliance celebrates the beginning of the 22nd century, with the induction of the 22nd colony world, Elysium.

X-COM has produced enough of the Thermal Superconducting material to begin constructing the mobile command station, codenamed Olympus. Timing of the project is intended to coincide with the last bit of the superconductor needed to finish the massive ship. Production is estimated to take 20 solar years.

The first Cydonian capital ship leaves its cradle from the Cydonian colony Litrella for Elysium. Likewise, the first ships wholly created by the Muton race arrive at Elysium in a symbolic gesture of celebration.

2130

Geological surveyors discover a cache of ancient alien artifacts on Mars. Subsequent archaeological investigation shows that the civilization that created them was a wholly different race from the Ethereals, and that it relied on a substance similar to Elerium. Information written into the artifacts points to what is translated as the "Mass Effect," and devices called "Mass Relays" for intragalactic travel. The First, Fourth and Sixth fleets are placed on high alert once it is learned that the closest mass relay used by the lost civilization is locked inside the Charon body.

The completion of Olympus is pushed back ten years to accommodate a change of plans and the introduction of anti-matter based weaponry. General Summers expresses great interest in seeing how the new weapons system would match up compared to the originally planned hypervelocity fusion lance.

2135

After years of tentative study, the Alliance decides to activate the Charon "Mass Relay." Doctor Vahlen, General Summers, and a newly appointed X-COM Director Jack Harper observe as the ice shatters and vaporizes while the artifact powers up. Astrophysicists record this as the first time that Dark Energy and its effect were directly observed. The Sixth Fleet accompanies a large expedition to see where the artifact will send them, and all are astonished to discover that they arrived almost instantaneously 36 light years away. Scientists note however that while impressive, sufficiently powerful Wormhole drives or gates (theorized, but never seriously developed) could do the same. This event jumpstarts the development of permanent Wormhole Gate installations, as X-COM is loath to risk using another alien race's transportation network.

Director Jack Harper is given clearance by General Summers to create a new organization within X-COM. This organization would "do whatever is necessary to ensure our survival, no matter how distasteful." In a moment of whimsy, the director and his chosen second, Eva Core, name their new division Cerberus.

Cerberus's first project is the implementation of Element Zero technology. While Elerium is superior to Element Zero for weapons technology, the latter can greatly reduce the power draw for ship movement and unlike Elerium's Gravity Wave effect can attract matter together.

Using his new authority, Director Harper commissions the construction of a stealthy mobile research center using deniable funding, with which to conduct operations isolated from X-COM and the Alliance proper. The ship is designated Tartarus.

2140

The first two Wormhole Gates are finished, and subsequently used to move the Charon Relay out of solar orbit. The deactivated artifact now sits nearly two thousand light years away in an area of dark space off the galactic plane, along with the second gate, remotely assembled and in a low power mode. More gates are ordered to be deployed to central colony stations with heavy military presence. These will form rapid deployment nodes for the Alliance Navy.

An exasperated Doctor Vahlen delays finalized construction on Olympus once again to implement Wormhole Gate technology into the massive super-dreadnought.

Director Harper proposes that while X-COM proper remains an elite rapid response force, there should be another more specialized force dedicated to dealing with potential rogues and terrorist organizations such as the dormant/defeated EXALT. Specific concerns are expressed at the possibility of rogue Psionic agents turning against the Alliance, as well as containing knowledge of humanity's potential from other possible enemies. General Summers approves the Extreme Conditions Unit, or X-CON. In later years, high ranking personnel will jokingly imply that the name has to do with the number of "pardoned" criminals serving time as lab rats in the unit.

Cerberus finishes development of the Combination Shield technology, which proves successful in blocking both kinetic impacts such as autocannon and missile fire as well as lasers and plasma. Fusion lances still can punch through, albeit with dramatically reduced effectiveness.

2147

X-COM develops a rapid-deployment variant of the Wormhole Gate for use by the Alliance Military.

The Olympus finally leaves Sedna Station, and promptly gates itself to the Alpha Centauri system to conduct shakedown testing. Afterwards, X-COM begins moving its headquarters and research facilities onboard the massive warship.

2156

Tartarus finishes construction.

In December, the First and Fourth Fleets return to Sol while the Second, Fifth and Sixth Fleets gather at Elysium in preparation for the Alliance celebration of the 150th anniversary of the Ethereal Defeat.

So, that right there is one reason why the Alliance will take some time to reinforce Shanxi.

As a result of drawing its roots from X-COM, the Alliance is quite paranoid and militaristic, a far cry from the original Mass Effect portrayal.