This story is based on XCOM: Enemy Within with the Long War mod.

Please note that the reviews contain major spoilers.

This story may contain material some may find disturbing.

This story is a sequel to XCOM: The Atlas Protocol

I do not own any characters explicitly mentioned in XCOM: Enemy Unknown/Within/2

Beta Reader (Chapters 0 – 12): Ashardalon125

Beta Readers (Chapters 13 – 23): BloodsplatBOOM, Ashardalon125 and Thuzan117

Beta Readers (Chapters 24 – 62): BloodsplatBOOM, Edumesh, Ashardalon125 and Thuzan117

Beta Readers (Chapters 63 – Present): BloodsplatBOOM, Edumesh, Ashardalon125, Aberron, HailtotheKing and Thuzan117

The are currently three spin-off stories written for this series by other authors, and mostly relate to subjects that appear as the story develops. It is recommended you read through Act III before starting them, but it is not required. All spin-off stories are considered canon in the in-universe continuity and are linked in my profile:

XCOM: New Blood by OfficialWeedTesterguy

XCOM: Pantheon Rising by Areleh

The Chronicles of Salvation by Edumesh

Galleries for Seals, Emblems, and Character Art from the series are linked in my profile due to the site not allowing direct links.

Dramatis Personae

(Please note that not all characters are listed)


The Commander – The Commander of the XCOM

Ariel Jackson – Central Officer of XCOM Analysis and Communications

Moira Vahlen – Head of XCOM Research and Development

Raymond Shen – Head of XCOM Engineering

Shaojie Zhang – Director of XCOM Intelligence

Patricia Trask – Overseer of XCOM Psionics Division

Abigail Gertrude – XCOM Intelligence Agent

Jamali Muhammad – XCOM Soldier

Sierra Morrow – XCOM Soldier

Aegis – Ethereal Defector

Zar'nartha'intha ("Nartha") – Vitakara Defector


Saudia Vyandar – Chancellor of ADVENT

Ethan Vyandar – ADVENT Protection Service

Elizabeth Falka – Director of ADVENT Intelligence

Richard Tygan – Lead ADVENT Geneticist

Ethereal Collective-Affiliated:

The Imperator – Leader of the Ethereal Collective

The Battlemaster – Commander of the Ethereal Collective Military

Zar'Chon'ravarian'vitiary ("Ravarian") – Zar'Chon of the Vitakara Zararch

Synopsis of XCOM: The Atlas Protocol

In the aftermath of the destruction of the alien Dreadnought, many different parties make moves to take advantage of the peaceful lull. The Council of Nations decrees to send a representative to keep an eye on XCOM and the increasingly independent Commander. As a compromise between the differing factions in the Council, Herman Diederick is chosen to represent the Council's interests and sent to the Citadel to begin reporting. In addition to sending a public representative, the Council also creates a secret counterintelligence squad led by a former UN assassin to keep an eye on XCOM and their covert operations.

Around the same time, the illusive, ancient, and secretive organization known as EXALT forges a faux alliance with the aliens, planning to utilize them to gain their technology and remove the ones they view as standing in their way of total world control: XCOM and the United Nations. The aliens accept their agreement and begin providing them with advanced tech and weaponry.

XCOM continues work on developing tech and tactics to use against the alien threat, and begin devoting resources to several new XCOM initiatives: Genetic Modification and the MEC Project, both heavily based on the alien substance identified as MELD. In addition, the Commander orders XCOM Intelligence to begin work to find out more about EXALT.

After stopping several alien attacks, EXALT lures XCOM into a trap and surprises them, taking out several of their best soldiers. Soon after XCOM Intelligence locates a shell company utilized by EXALT, and eventually locate one of their hidden bases with the help of the Council Shadow team. With the advantage of surprise, and the new MEC troopers, XCOM easily wipes out the EXALT installation.

Soon after the raid in EXALT, the Commander receives an offer from the President of Russia to visit, and they form a secret alliance, planning to send resources through proxy countries to circumvent the restriction on trading alien tech with Council Nations. Through this XCOM forges alliances with several more countries, including Ukraine and Armenia, much to the dismay of the Council, who are further antagonized when the Commander orders an airstrike in Newfoundland to destroy a chryssalid breeding ground.

Soon after that, Dr. Vahlen begins applying her genetic modifications to XCOM soldiers, after first performing experiments on prisoners to weed out adverse effects, and they prove to be extremely effective against EXALT and alien forces. Israel also begins acting suspiciously and XCOM Intelligence is directed to determine the reason for it. After infiltrating an Israeli military camp, they retrieve several major documents, including one entitled Operation: ADVENT, which detailed Israel's plans to start a war with various Middle Eastern nations.

EXALT suffers several defeats at the hands of XCOM, prompting the aliens to begin questioning if their alliance is truly beneficial. Several times they remove psionic subjects that EXALT is experimenting on for their own purposes, though one escapes and EXALT sends out people to track her down.

Following a failed attempt by EXALT to discredit XCOM, the Supreme Leader of North Korea contacts the Commander, and after some negotiations, agree to join as an ally of XCOM. Shortly after that, an Ethereal by the name of Aegis telepathically contacts the Commander, and reveals the location of one of EXALT's major bases. XCOM acts on this information, and takes control of the base and speaks for the first time with the Director of EXALT.

Due to the EXALT base being in China, and previous tensions between them and XCOM, China withdraws from the Council and pulls their funding. In response the Commander allies XCOM with Taiwan and ASEAN. Shortly after, an XCOM soldier turns himself into custody, revealing himself to be an alien infiltrator, and provides XCOM with a wealth of information, including the location of an alien base controlled by Sectoids on Earth. XCOM sends two squads to assault the base and they take it successfully, though suffer serious losses at the hands of a deadly psionic Hive Commander.

After the loss of their base, and EXALT consistently losses to XCOM, the Ethereals take a direct interest in EXALT and send down the Ethereal known as the Ravaged One to direct EXALT to their specific goals. The Ravaged One then lures XCOM into a trap and easily wipes out the squad, warning XCOM to surrender or face a war with the Ethereals.

Just after XCOM recovers from that attack, the Ravaged One launches an attack on New York, one that takes the lives of several more soldiers, and hundreds of thousands of civilians, but is ultimately driven back with the combined might of XCOM psions, soldiers and the local police and soldiers. EXALT at this point decides to put in motion their plan to betray the aliens, having made a tenuous truce with XCOM earlier for the sake of the world.

With the world in a precarious position, the Commander reveals the Advent Directive; his plan to replace the United Nations and establish a world government with true power and authority, one which XCOM would be an ally to. He convinces multiple countries of the necessity, and prepares to unveil it when the time is right.

The aliens decrease their attacks, giving XCOM a brief period of peace which is shattered when the Ravaged One leads an attack directly against the Citadel, killing nearly a third of XCOM's soldiers and several of their command staff before being killed by the combined might of the XCOM psions.

After the unsuccessful attack, EXALT puts their plan in motion to destabilize the world as a final requirement for their alliance, and manipulates Israel and Brazil into going to war with nearby nations, threatening to throw the world into chaos as the aliens prepare a retaliation. Soon after the Commander himself meets the Director, and he requests that she take command of the new ADVENT organization and disperse the remaining EXALT members into its ranks for the greater good, on the condition that EXALT has to die forever. She agrees and prepares to take control of the new world government.

It ends with the aliens launching an all-out attack on Australia and taking the continent. At the same time XCOM responds to an abduction report and discover the Ethereal Aegis waiting for them who turns himself into XCOM custody. As the aliens continue to stabilize Australia, the world frantically attempts to ready itself for a war they are unprepared for and the Commander wastes no times in preparing his first response, starting with the execution of the Demeter Contingency.