Game opens with you being rescued from an alien facility, where they have implanted a chip into your brain, and the resistance removes this chip. During the procedure, you experience several "flashbacks" to when the aliens put it in in the first place.
This immediately triggered the thought in my head: Are we really seeing the truth, or am I under mind control, the implanting being made to look like a rescue? The lineup of the flashbacks with the 'normal' views is near perfect. Too perfect.
It's explained you've been out 20 years, and the Aliens won. They now use Advent to control the human population, which provides us with the primary enemy for Xcom 2. What aliens we do get to see are in support or leadership roles, usually with 2-3 advent troops.
So, analyzing Advent, they are a military organization which have combined human and Alien DNA to form superior soldiers, and also field MEC troops. This triggered another red flag immediately for me. Xcom Enemy Within, you injected Alien DNA into your troops to enhance their abilities, OR cut them to ribbons to surgically create MEC troopers.
Is Advent really Xcom? Am I really fighting for the Aliens?
Advent's goal is to create an AVATAR: a super psionic soldier, and they are screening the population for the best candidates. Xcom: Enemy Unknown and Enemy Within, this was Xcom's goal. Creating The Volunteer, a super psionic soldier, and they went about screening all their soldiers...
You no longer have a base, but instead fly around in a UFO, and launch clandestine operations in city centers, or defend your assets from Advent attack. Is this not what the Aliens have done in previous games?
And then there are fragments of story that pile up and just don't make a lot of sense.
Our lead scientist has a huge, obvious scar on the back of his head. The most likely explaination I can come up with is he's been implanted as well. All other 'main' characters have hair that hide potential scars. However, it's explicitly stated that you are the only one to ever survive this chip removal operation. Is the scientist still implanted? Where did his scars come from? He admits to having worked for Advent at the beginning, and even worked on these chips. Why is no one asking?
Our old lead scientist is alluded to, but never found. Yet, it's clearly her work in the advent soldiers. Why was this left hanging?
I don't think it's necessarily scripted, as a technically random 'dark event', but very likely you are going to get shot down at some point. The ensuing mission, it's explicitely stated, THEY DON'T WANT YOU, THEY ARE TRYING TO CAPTURE YOUR UFO. Now, if Advent/the aliens are really in charge, WHY would they want to kill everyone to capture what is supposedly an older UFO model? Is this not exactly what Xcom would do? There is no good reason for the aliens to capture and not destroy outright. This is either poor writing or a huge clue that you are really the aliens this time around.
In our final mission, the "elders" make a bit of an appearance, as you face a couple enemy Avatars. They pretty much come right out and ask you to stop being manipulated and return to them. Going to far as to say you've defeated "them" (meaning the people you are now working for) before, you can do it again.
We are left with what appears to be an obvious setup for a terror from the deep remake as something starts being active in the ocean depths.