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Fanfic / XCOM: The Atlas Protocol

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XCOM: The Atlas Protocol is the second story in Xabiar's XCOM: Enemy Unknown fanfic trilogy. Like the previous story, XCOM: The Hades Contingency, it is based on Enemy Within with XCOM: Long War and some XCOM 2 elements.

The story takes place after the (mostly) successful execution of Operation: Gangplank (the downing of the alien dreadnought over China). As XCOM continues to fight the alien incursions, the Council of Nations, wary of the Commander, send in a liaison to keep watch over him, while Patrick Rush assembles a team of intelligence operatives to investigate his actions.


Behind the scenes, the shadow organization known as EXALT, intent on uniting the nations and people of Earth under one banner, strikes an alliance with the alien invaders in order to harness their technology.

This story concludes in XCOM: The Advent Directive.

Note: This page contains unmarked spoilers for Hades Contingency.

This story contains examples of the following:

  • Abusive Parents: Chapter 35 reveals that Creed had an abusive mother who would cut his younger brother for any offense.
  • Adaptational Badass: Ethereals were worthy endgame foes in canon, but still very much beatable if you knew what you were doing. Here, their powers are very much on display and they are the stuff of nightmares.
  • Adaptation Expansion: EXALT, in canon, was a nebulous organization supporting the aliens for no clear reason. This story vastly expands on their internal structure, culture, and motivations.
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  • Anyone Can Die: Oh boy... Even Mission Control is not safe now. Bradford and Van Doorn of all people are killed in the Base Assault.
  • Badass Teacher: Chapter 20 reveals that before Ruth formally joined the Kidon, she was a teacher who used her position to spy on the parents of her students who had criminal connections.
  • Be Careful What You Wish For: EXALT wants to rule the world? The Commander gives it to them via Advent... For the low, low price of having to come out of the shadows.
  • Body Horror:
    • The results of the failed MELD experiments are... not pretty, to say the least.
    • In chapter 31 we see the grotesque results of the experiments the aliens have been conducting on human captives.
  • Chekhov's Gun: Early on, after Myra gets turned into a MEC Trooper, Patricia notes that she's nearly invisible to psionic detection now. In chapter 36, this allows her to surprise the Ravaged One.
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  • Dirty Business: Abby hates some of the extremes she has to go to in her intelligence work.
  • Don't Make Me Destroy You: In chapter 35 the Chronicler gives Cerian and team a final warning when they break into his apartment.
  • Dramatic Irony:
    • The Fictional Document at the end of chapter 13 says that no documented evidence exists of a perfected third generation thin man. The Advent speaker presumably is one. And so is "Soran", as chapter 30 reveals.
    • In chapter 17, the Commander expresses the hope that EXALT didn't extract information from his previous subordinates and declares his intention to avenge them. Earlier in the story, it was revealed that EXALT did just that, but not in the way he was probably expecting.
    • In chapter 20, one of Cerian's operatives wonders why Russia hasn't approached the Commander to directly ally with XCOM, not knowing that just that happened a few chapters back.
    • In chapter 43, Patricia remarks that only XCOM and the aliens have psionics, unaware that the Chronicler is one. The Commander makes the same mistake in chapter 46.
  • Early-Bird Cameo:
    • Lily makes her onscreen appearance after having been foreshadowed in the previous story.
    • The representative the aliens send to EXALT is the ADVENT Speaker. Well, technically without the ADVENT part.
    • One of the projects Shen suggests in chapter 9 is the EXO Suit.
    • Tygan gets mentioned by EXALT as a potential recruit in chapter 10 and appears onscreen in chapter 18.
    • Israel is working on Magnetic Weapons, armour that uses alien alloys, and has a plan name that translates as "Advent". Gee, that doesn't sound familiar at all...
    • And on top of that North Korea is also making armor from alien alloys. Specifically, Advent Trooper and Advent Officer armor.
    • In chapter 41, it is mentioned that America has started work on humanoid autonomous robots inspired by MECs.
    • Andromedons appear in chapter 42.
  • Enemy Mine; In chapter 45, XCOM and EXALT forces attack the alien base in the Arctic.
  • Even Evil Has Standards: When the talk of using Chryssalids comes up in chapter 14, some members of EXALT are disturbed by it.
  • Evil Counterpart: The Advent Speaker is this to the Council Speakers, being the link between EXALT and the aliens. He even ends their communications off with the same "We will be watching" catchphrase.
  • Evil Is Not a Toy: EXALT believes that they can manipulate and betray the alien invaders the same as they can human groups. This is decisively not the case.
  • False Reassurance: In chapter 35, Abby and Jochern offer to "take care" of a captive.
  • Gambit Pileup: In chapter 3, the Council sets up a counterintelligence group of its own to look for dirt on the Commander and XCOM, and later it's revealed that certain persons of interest to them are actually EXALT operatives.
  • Hidden Agenda Villain:
    • The mysterious alien who nicknames itself "Aegis" has been feeding the Commander information in his dreams for reasons only it knows.
    • As we learn more about the Chronicler, it becomes quickly apparent that we don't know what his endgame is, and it may not even fully align with his EXALT masters. In his last appearance as of this instalment, he psionically manipulates Cerian's team and XCOM into attacking each other, with the end result of further intensifying XCOM's mistrust of the UN... but to what true end remains unknown.
  • Idiot Ball:
    • Overlaps with Genre Blindness. Cerian, a mysterious man who can effortlessly (and impossibly) guess your every move, has demonstrated freaky mind-powers beyond your comprehension and has let you and your team go multiple times despite clearly demonstrating an ability to wipe you out with no evidence at any time, and your best idea is to try and assassinate him?.
    • The Council of Nations suffers this big-time. Lampshaded by the Commander just before he kills them. Nobody in their sane minds would believe that a war criminal with a serious grudge against them and absolutely no reason to listen to them would magically decide to become an obedient puppet after being put in-charge of possibly the most powerful government organisation in human history.
  • If I Wanted You Dead...: In chapter 40 the Imperator tells Patricia that the aliens are not at war with mankind, because if they really were, Earth would already be cinders.
  • Imperial Stormtrooper Marksmanship Academy: Played With and actually justified with the larger battles. While battles against psionics incur roughly the same number of casualties as an average player, the majority of the battle is actually mental in nature. The soldiers have trouble aiming when they are constantly bombarded with emphatic attacks and psionic blasts since psionics have been vastly upgraded in this fanfic, rather than being "elite" forces who can't hit the broad side of a barn.
    This is best exemplified with the soldiers who are immune to fear, such as Myra, who mechanically slaughters every enemy, psychic or not, in every battle she takes place in, making her (and other MECs) the most effective soldier bar psionics by a country mile.
  • Liberty Over Prosperity:
    • In chapter 26, North Korea's Supreme Leader gives a speech to the Commander that essentially boils down to asking if chaotic freedom and democracy are really preferable to an orderly and prosperous dictatorship.
    • The Commander himself subscribes wholeheartedly to the inversion (even beyond what EXALT would consider), as seen in his Advent Directive.
  • Linear Warriors, Quadratic Wizards: Psionic powers are shaping up to be this. Based on alien plasma technology, we already know the probable maximum limit XCOM will reach technologically. Psionic powers have only recently been introduced and the only people who can even TOUCH psionics are other psionics. That is not even scratching the ability to unconsciously wipe out an entire EXALT base, see enemies through walls, and kill the entire population of a city just by being there.
  • Mistreatment-Induced Betrayal: It's revealed that EXALT managed to save several of the Commander's men from execution by the UN, and they promptly joined up.
  • The Mole: After the first battle with EXALT, the Commander deduces that EXALT knows a bit too much about countering XCOM's gear and tactics to not have an inside man; the question is who... As chapter 30 reveals, it's Soran, who's actually a perfected thin man. Then it's later revealed that the Council Speaker is one too, working for EXALT.
  • Mugging the Monster: In chapter 21, two gangbangers make the mistake of trying to mug Annette.
  • Mythology Gag: In chapter 29, after learning that Creed has an interest in Alternate History fiction and is planning on going into writing after the war, Patricia suggests that he could write an ATL where the aliens won only for mankind to revolt afterwards.
  • Not So Different: In chapter 36, the Ravaged One says this of Patricia.
  • Oh, Crap!: Ethan freaks out in chapter 28 on learning that XCOM's Commander is his former Commander.
  • One-Man Army: Ethereals. In chapter 30, it is recounted how the subjugation of the mutons was led by one ethereal who started off by singlehandedly using a sword and its psionics to cut down much of a tribe.
  • One World Order: In chapter 37, the Commander lays out his plans for an Advent Administration to unify mankind to properly stand against the alien invasion.
  • Power of Trust: In chapter 35 when Patricia tries to get a trapped-in-his-own-mind Creed to refrain from killing the mental representation of his abusive mother, Creed states that even though he can't remember who she is, he somehow feels that he can trust her and complies.
  • Previously On…: The first chapter includes a recap of what happened in Hades Contingency.
  • Professional Killer: Cerian considers himself an Assassin.
  • Required Secondary Powers:
    • In chapter 9, Shen expresses concerns about the MEC programme because the augmentation needed for a soldier to use a MEC effectively would be so invasive both in brain and body that any MEC troopers would not be all there outside the suits. While he thinks this issue might be resolvable with time, time is not what they have.
    • Increasing squad size isn't simply a matter of buying an upgrade from the Officer/Guerrilla Training School, but requires the Skyrangers to be modified to accommodate the extra members, which takes time and resources. In addition, a separate Skyranger has to be specially built for transporting MEC troopers.
  • Somebody Else's Problem: In chapter 31 this is actually weaponised by the sectoid Hive Commander.
  • This Is Impossible: In chapter 44 Aegis tells the Commander that the killing of an ethereal should not have happened.
  • This Is Reality: In chapter 44 the Commander says in a dream to his dead wife that this is reality and no one person can save everyone.
  • Title Drop: The Atlas Protocol - the plan for when the Citadel comes under attack.
  • Total Party Kill: In chapter 33 this happens to the XCOM squad sent to investigate an alien abduction that turns out to be an ethereal entering the field.
  • Villain Episode: Several chapters show EXALT perspectives.
  • We Have Become Complacent: In chapter 25, Ethan says that EXALT has gone too long without fighting someone who was actively trying to destroy them, as opposed to someone who merely learned of a proxy plot and tried to thwart that.
  • Weak, but Skilled: In chapter 27, Creed demonstrates to Carmelita that a sufficiently skilled baseline can still defeat a Genemodded trooper in melee.
  • We ARE Struggling Together:
    • In addition to the Council, it turns out even the Aliens are not immune to this. Different Ethereals have different ideas on subjugating a species. The previous Ethereal (presumably the one encountered in the video game, advocating gradual improvement of technology to test humanity) is replaced midway by one who favours a more direct approach. Really the only reason why the Ethereals are not fighting among themselves is that the chances of meeting one another are so slim.
    • All this not counting Soran's rebellion.
    • The only major organisation seemingly immune to this is EXALT.
  • Wham Episode:
    • Chapter 12. XCOM meets EXALT in battle for the first time. Despite managing to get some kills, the squad is forced to retreat without even being able to recover their dead.
    • Chapter 26. North Korea's leader contacts XCOM to propose an alliance and have alien tech of their own, including a UFO they had managed to down and capture.
    • Chapter 33. Following its "visit" to EXALT at the end of the previous chapter, the Ravaged One carries out a Total Party Kill on an XCOM squad and announces that the aliens are stepping up their invasion.
    • Chapter 48, the final chapter. Where do we begin. Australia is under all-out alien attack, with at least two ethereals involved. X-Com's squad encounters another Ethereal. This Ethereal effortlessly dismantles the squad that managed to take down the Ravaged One, proving that he wasn't even the most powerful... then surrenders to X-Com.
  • Wham Line: In chapter 46.
    "I want you to lead it."
  • The Worf Effect:
    • In chapter 29, the Chronicler shows exactly why he's someone to be feared by showing Cerian that he already knows about his group and their plans for Solaris Industries.
    • During the attack on NYC and the Base Defence, the Ravaged One overpowers and kills several of XCOM's psionics, including none less than Annette.

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