So at the end of the game, there is a clear psi disturbance at the bottom of the ocean. This suggests some kind of Terror from the Deep. I don’t think it will be same story line as the original Terror from the Deep.
The Elders during the last mission state that there is something which has followed them, and will now follow you (unsure whether they mean humanity of the Commander). This something has consumed them and ultimately destroyed them. The efforts on Earth were to find a way to stop them by combining human DNA (which apparently is awesome) with themselves to produce the Avatars.
Also, throughout the game, there are few hints with respect to Dr. Vahlen. The detection of German comm traffic. Shen finding notes written in German. Shen gets reports of creaking in the forward bulkheads (she sure hopes it isn’t metal fatigue), I’m not sure whether this one is Vahlen related or not. I think Vahlen might be on the Avenger (sneaking around, hence the creaking). But what could she be up to??? Why wouldn’t she still be part XCOM / the resistance??? Does she know something about Tygan? I still don’t trust that guy for some reason.
Any thoughts on what the future might bring either for an xpac or the inevitable XCOM 3?