XCOM 2: The Lilith Project

It's been 20 years since the fall of XCom Headquarters and the last sighting of the Commander. For two decades the loss has haunted Central Officer John Bradford. He has tracked down whispers and ghosts all over the globe to correct what he sees as his biggest failure, not being at his post when the Commander needed him the most. What could spur such honor, devotion and loyalty?

XCOM 2: The Lilith Project is an Alternate Universe Fan Fiction by Asukanerv002 that follows the events of XCOM 2 with a few key differences. Most notably, the Commander is explicitly female, with Bradford in particular having a relationship with her that goes past professional. But as the story unfolds, however, it becomes evident that there's more to ADVENT, the aliens and the Commander's captivity than meets the eye.

The fic, which is still in progress and at points NSFW, can be found here.

Tropes used in XCOM 2: The Lilith Project include:

Adaptation Expansion: Of sorts, as the fic does shed more light on Bradford's days drowning his sorrows following the Alien Invasion's success and the rise of ADVENT. The opening chapters also expound on the Commander's rescue from Bradford's perspective.
Adaptational Villainy: Not only is Dr. Vahlen much less sympathetic this time around. But it's revealed that she raped Bradford in the immediate years after the Commander's capture, all so she could get the necessary "data" for Project Lillith. That she expressed heavy regret for her actions in her German notes notably makes the Commander even more eager to kill her if given the chance.
Alternate Universe Fic: Though the story still more or less follows the events of the games, there hare certain differences from canon that gradually become more obvious as the plot goes alone.
The Chains of Commanding: The Commander does have a good head on her shoulders and has proven herself to be more than capable, it's also shown that it comes with a heavy price. As sending men and women to possible die with the fate of mankind at stake does weigh very heavily on her.
Everyone Calls Him "Barkeep": While the Commander does have a name this time around (Margaret/Maggie Curtis), most everyone else in XCOM refers to her either by her title or some variant of "Mum." Bradford's among the only ones who are on a first-name basis with her, and vice versa.
Fish Out of Temporal Water: Downplayed, as the Commander forces herself to get up to speed with "current events," and it's not like she has any love for what's being passed for modern culture by ADVENT. Though she does note how the wardrobe and artefacts Bradford, Shen and the others managed to salvage are a few decades out-of-style.
Four-Star Badass: Subverted. XCOM's first commander, William J. Rivel, is described in the backstory as a distinguished general and having served in the U.S. Army. Unfortunately, while doing as good as job as he could manage, the true threat posed by the Alien Invasion prompted the Council to replace him with the current Commander.
Generation Xerox: It's eventually revealed that sharpshooter Lt. Bo "Dragon" Zhang is the son of Shaojie Zhang from Enemy Unknown, but forgoes any preferential treatment in favor of wanting to succeed by his own merits. It's also mentioned that he even closely resembles his old man.
Mauve Shirt: Given that this is still XCOM, most of the personnel and soldiers can be seen as this, as they all have names and personalities. It's also not guaranteed that any given character out on the field is going to make it back to the Avenger in one piece. This is especially true of "Gamma Squad" which is shown to have more casualties owing to being host to more green recruits.
Mildly Military: While the Commander does have a CIA background, this is the reason why the Council of Nations chose her to assume command of the XCOM Project back in the events of Enemy Unknown, as it was thought that a purely military response to the Alien Invasion was woefully insufficient. In the story, she herself coyly lampshades how the contemporary XCOM might benefit more from more professional military-style discipline.
Old Shame: In-universe, Bradford considers the immediate years following the Alien Invasion to be this. For more reasons than one, and enough that he forces himself to remember them.
Older Than They Look: Thanks to the stasis suit ADVENT and the aliens encased her in as well as the circumstances behind her imprisonment, she still looks to be in her twenties whereas Bradford is 20 years older.
Posthumous Character: In addition to Dr. Raymond Shen, it's revealed that Shaojie Zhang is also long since dead by the time the story takes place. Having suffered a fatal injury from an alien grenade during the fall of XCOM Headquarters.
Secret Keeper: It's strongly implied that Dr. Raymond Shen knew of the budding relationship between Bradford and the Commander and may have told his daughter Lily at some point.
Title Drop: It takes several chapters in before the titular Project Lilith gets namedropped through Vahlen's notes. It's also hinted as being closely tied to the Avatar Project.
Tranquil Fury: How the Commander's resolve to kill Vahlen should their paths meet for both her collaboration with ADVENT and her raping Bradford ultimately settles down on.