Lord Raine said:
I'm getting pretty hyped up about XCOM. I kind of want to see a fic where Shepard is The Commander. He drags humanity through terror and extraterresterial warfare, pioneers research into alien technologies beyond our understanding, and becomes a living legend. The Archives on Mars are discovered, and Shepard pushes to decrypt as much of them as possible to fortify Earth's solar system. Hostile aliens find out and invade with the intent to capture the Archive and destroy Earth once and for all. Shepard and the XCOM forces repel them in direct hard contact, but Shepard is mortally wounded in the process. XCOM and the Earth Defense Force puts the dying Shepard on ice until such a time that they have the technology to heal him.
Fast forward to Mass Effect 1, with a much more paranoid and technologically advanced Earth, a galactic power in their own right, bringing "The Commander" back from cryo. His mission? Serve as a Spectre candidate as a diplomatic gesture towards the Galactic Council, while simultaneouly establishing and training a new elite force to protect and defend Earth and all her colonies.
That force? The N7 Project.
After beating XCOM on Normal (I'll try the harder modes later) I present the following idea.
Warning Spoilers for XCOM ahead.
During the Endgame, the Big bad's reveal that XCOM's success was exactly what they hoped for all along. As you fight you're way through the ALien Complex that reveal that each of the races you engaged was something they found and attempt to uplift in an effort to fight a greater evil. The fact that a Squad of Humans (Lead by a powerful Psionic) has kicked the door in and is laying waste to their failures justifies the attrocities they commited, in their minds.
Their plan worked to well and the humans end up slaying the Big Bad's (who admitted to being the biggest failures since they were rejected by another power) while the try to convince you that humanity needs their guidance.
So since the Protheans are confirmed to be a mix of races we'll say that these guys were the last remnants of that ancient empire. They've been traveling around the galaxy ever since trying to build an army that could stand against the Reapers while developing tech that is not based on Reaper designs.
Adrian Shepard, was a talented Assault trooper that joined the XCOM directive early and eventually rose to lead 95% of the ground missions. Elisa Harper was the woman in overall charge of the XCOM project. The two didn't always agree on how things should be done, but they bother were determinted to protect humanity.
Anyways, Shepard is discoverd to have Psionic potential and is eventually turned into humanities first Psionic warrior (I envision this Shepard using the Alloy cannon manily because of rule of cool). After the endgame Shepard appears to be lost and the XCOM project is official shut down now that the threat has pasted.
Elisa Harper has other ideas.
XCOM is reborn under the name 'Cerberus' and works quietly behind the scenes as humanity takes it's first steps towards the stars.
Since Adrian Shepard died during the final battle Cerberus puts into place a Long term plan. Since they have his DNA and Elisa Harpers' they work to combine them, and create a warrior to lead humanity out into a dangerous galaxy.
Elisa Harper lives out her life, eventually giving birth to children. Her line eventually resulting in Jack Harper who eventually becomes 'The Illusive Man'.
The 'Shepard' Project is completed before TIM takes control and without his knowledge. The 'XCOM' cell within Cerberus then secret the child away, raising him on a colony world and slowly helping him master his Psionic gifts and teaching him how to lead without him ever realizing his true nature or purpose.
The Batarian's attack, and Shepard loses his family, but manages to save half the colony using his gifts.
The Story would proceed from here.