Work Header

XCOM: The Atlas Protocol

Chapter Text


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


This story may contain material some may find disturbing


This story is a sequel to XCOM: The Hades Contingency


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


Beta Reader: Johnclaw Dragonhelm


Dramatis Personae

(Please note that not all characters are listed)

            The Commander -       Commander of the XCOM Project

            John Bradford -           Central Officer of XCOM Analysis and Communications

            Raymond Shen -          Head of XCOM Engineering

            Moira Vahlen -            Head of XCOM Research and Development

            Shaojie Zhang -           Director of XCOM Intelligence

            Peter Van Doorn -       Tactical Advisor to the Commander

            Abigail Gertrude -       XCOM Intelligence Agent

            Patricia Trask -            XCOM Squad Overseer

            Annette Durand -        EXALT Test Subject

            Patrick Rush -              United Nations Liaison

            Saudia Vyandar -         Director of EXALT


Synopsis of XCOM: The Hades Contingency

In December of 2014 the entire population of a small town in Florida went missing without a trace or explanation. Publically, the incident was covered up and silenced when a powerful subsection of United Nations, known only as the Council of Nations, quietly stepped in. The Council discovered that their worst fears were coming to pass, what had happened was the result of alien activity and that only meant one thing: An invasion was coming.

In response, the Council officially activated the XCOM Project, a secretive paramilitary organization created specifically in the event of an extraterrestrial invasion. Despite being more advanced than the militaries of Earth and composed of the best soldiers in the world, the Council knew that they would need someone to lead it. Someone who would do whatever to took to defend the human race.

One such person existed. Only known as the Commander, he’d been imprisoned by the United Nations for nearly a decade for war crimes committed in a crusade against terrorism. A brilliant, deadly and ruthless leader, the Council knew that he dangerous, but also knew he was their best chance to survive. His appointment wasn’t without conflict, but eventually the Council allowed the Commander to assume control of the XCOM Project on the condition that he would answer directly to the Council.

The Commander accepted and immediately began working to increase the military and technical strength of XCOM. The first few months involved multiple alien abductions which the Commander responded to by sending squads of soldiers to investigate, though despite their expertise, not even XCOM was able to keep their missions free of casualties. But with each successful mission, XCOM learned more from their technology and utilized that knowledge to its fullest potential.

Throughout this time, the Commander began working to implement an Intelligence division into XCOM, though time constraints and other responsibilities prevented him from doing so. The Council quickly learned that the Commander was not the obedient subordinate they had hoped as he flatly refused to supply the Council with alien technology recovered and further antagonized them when he refused to turn in Shaojie Zhang, a man wanted by the Council. Not only did he refuse to follow the directive, he appointed Zhang Director of the new Intelligence Division within XCOM without the Council’s knowledge.

Despite victories against the aliens on the ground, the extraterrestrial beings made their influence known in other ways. XCOM soon realized that Germany was targeted by the aliens for destabilization. Within weeks the country was whipped into a state of fear and the Commander had Zhang use his agents to determine the cause.

In anticipation for the worst, the Commander began making alliances with high-ranking German military leaders as well as gaining the support of non-Council nations such as Israel in exchange for alien technology to expand XCOM’s influence and authority.

After capturing several people responsible for the destabilization of Germany, they were interrogated and revealed that not only had the aliens been responsible, but the Council as well, though it appeared to have not been the original intention. Another mysterious organization was also identified, though the Commander only learned a name: EXALT.

The events in Germany culminated with the aliens attacking Hamburg and massacring thousands of civilians before XCOM was able to stop them, losing several more soldiers in the process. Fearing another attack, Germany withdrew from the Council and began negotiations with the aliens. In response, the Commander initiated the Hades Contingency, a final effort to ensure the country didn’t fall under alien control.

Despite the high civilian casualties, it succeeded and the Germany became an official ally of XCOM, much to the chagrin of the Council, some of whom made their opposition more public. In response, the Commander learned the name of a Councilor allied against him and paid the councilor a visit, threatening to expose his involvement in Germany if they continued interfering.

The following months involved a massive offensive against the alien forces where the Commander led XCOM to a string of several major victories against the invaders. Alien transports and UFOs were shot down and raided mercilessly, though the list of dead soldiers continued growing as well. In response to these victories, the aliens sent a dreadnaught to China with the intent to raze the city.

XCOM learned of the impending attack and quickly assembled a squad of their best soldiers. In coordination with the Chinese and Japanese military, they diverted the dreadnought and boarded the ship. Despite suffering heavy casualties, the XCOM soldiers crashed the dreadnought into a city. Removing the threat, but also killing almost a quarter of the population.

Realizing the Commander had been given too much autonomy, the Council sent a representative to reestablish their authority and ensure their will was known.  A week after the attack, an alien substance that had been recovered throughout the war was thoroughly researched and dubbed as MELD by the science and engineering divisions. The Commander immediately ordered then to begin work on implementing it into their arsenal. Meanwhile, the enigmatic organization known as EXALT prepares to move against XCOM, though not before gathering allies.