|Spoilers for The Bureau: XCOM Declassified follow.|
Waiting in a room at the Groom Range facility for Director Faulke's summons, William Carter meets a military officer who informs him that she is to escort him to Faulke to deliver a briefcase. When a wary Carter refuses, a black fluid discharges from the officer's eyes, revealing herself to be "infected"; she then shoots Carter and opens the case. It emits a blinding light which incinerates the officer and stuns Carter. Moments later, Carter awakens to find his gunshot wound inexplicably healed and the case destroyed as the base comes under attack. Carter attempts to rescue Faulke as the attackers, identified as "Outsiders" by Bureau agents whom Carter encounters, easily slaughter the base's garrison. He eventually finds Faulke, but is too late to save VIP officials J. Edgar Hoover, CIA Director Frost, and General Deems, the latter of whom had become infected like the female officer and killed the other officials. Carter escapes the Groom Range facility by tram just as Outsider devices cause the mountain to implode, and stalls the Outsider pursuit by detonating a powerful Elerium bomb while he and Faulke flee via Skyranger helicopter.
At the Bureau's command bunker, Faulke announces that communications worldwide have been jammed and other U.S. military bases have been destroyed in similar attacks. With no way to contact the White House and other American military leaders, Faulke formally activates the Bureau and assumes control of the country's remaining military forces to counter the Outsider threat, while Bureau operatives planted in major cities downplay the attacks as safety drills to keep the civilian populace from panicking.
Over the following weeks, Carter leads teams of agents across the country to retrieve important personnel, defend strategic sites, and recover what alien technology they can for research. Gradually, the Bureau pieces together the Outsiders' motive: to conquer the Earth and terraform it into a new homeworld, simultaneously enslaving humanity. The interrogation of an Outsider Infiltrator reveals that their species is commanded by an entity known as Origin through a psionic network called Mosaic. Carter's team travels through a "Venn Portal" to their homeworld using the Avenger, a spacecraft XCOM has developed. There, Carter discovers that Mosaic is powered by an enslaved Ethereal, a being of pure energy with immense psionic power. The Outsiders have been searching for a dormant Ethereal on Earth, which is revealed to have been inside of Carter's briefcase from the game's opening and now inhabits his body. He manages to capture Origin's Ethereal, detonates a bomb at Mosaic's entry point and returns to Earth.
At XCOM's base, the captured Ethereal, Shamash, psionically contacts the Ethereal inside of Carter, Asaru. It becomes apparent that the player has actually been playing as Asaru, who has in turn been psionically controlling William Carter, though its recently awakened state caused it to believe it truly was human. Shamash claims that because both the Outsiders and humans have learned how to capture Ethereal, they must be destroyed so that a force like Mosaic will never be rebuilt. Upon hearing this, Carter manages to temporarily break free of Asaru and kills Shamash. XCOM's base is discovered by the Outsiders, and Carter attempts to defend it, while actively attempting to break free from Asaru's control. Carter manages to plant an explosive device with a thirty second timer, believing that the Ethereal will never truly allow him to be free.
There are four endings depending on choices made at this point. If Asaru refuses to relinquish control of Carter, the bomb will go off, killing both of them.
Alternatively, Asaru can release Carter, but only to willingly merge with either Dr. Weir, Agent Weaver, or Director Faulke. The new host will knock Carter unconscious and the remaining agents abandon the base in the Avenger. They discover that Origin still exists within what remains of the Mosaic network, and has transported itself to Earth's orbit in order to command the Outsiders stranded on the planet. The crew of the Avenger mounts their final attack against Origin's ship, with Asaru providing the new host with the powers it had given Carter. During the mission, one of the other two host options must be sacrificed while the other is rescued, and Carter, who believes that Asaru is no different from the Outsiders, must be either executed or incarcerated. Eventually, Asaru's host discovers a secondary entry point for Mosaic and psionically integrates with the network, destroying Origin and its influence over the Outsiders.
The aftermath of the Outsider invasion is revealed in the form of a debriefing of Asaru's host.
- If Weir merges with Asaru, he persuades the Outsiders to cease attacking and help rebuild before departing amiably to continue their search for a homeworld; Outsider technology is carefully disassembled and stored away, sites of Outsider attacks are quietly erased from the National Register or explained away as natural disasters, and surviving Sleepwalkers are cured.
- If Weaver merges, she forces the Outsiders to kill each other; all Outsider technology and evidence of their attacks is destroyed, in some cases with nuclear weapons, and the Sleepwalkers are euthanized.
- If Faulke merges, he commands the Outsiders to stand down and rebuild before being exterminated; some Outsider technology is preserved and provides considerable scientific and military advances, sites of Outsider attacks are erased, and the Sleepwalkers are treated, but unable to be cured if you don't go to save Weir in last mission.
In the end, the Outsider invasion is successfully covered up, with only the members of XCOM and a handful of top U.S. and other world leaders aware of how close the human race came to extinction.
The debriefing concludes with a description of how Asaru eventually severs contact with its host and departs after the Outsiders are dealt with, and its intentions remain unknown. At this point, the musical score segues into a theme from XCOM: Enemy Unknown.