Board Thread:Questions and Answers/@comment-23371555-20150902203820/@comment-24729554-20150903201052

From what the devs have said so far, all of them are considered canon to an extent. Here's a quote from MD's gameplay director about this:

"We did what the original Deus Ex did with its sequel. All the endings kind of happen. A little bit of everything happened because that's the way these things kind of turn out to be," (a bit vague, but yeah..)

The self-destruct ending is at least partially canon since Panchaea has definitely been destroyed. However, Jensen obviously didn't die during this event for some unknown reason. Going by what we've seen about Mankind Divided, I'd say ideology-wise, the closest to canon is a combo of Darrow's and Taggart's. Augmentations are feared and restricted as Darrow wanted, but the Illuminati still manage to cover their involvement and come out on top regardless of what Jensen chose. I'd say Sarif's makes the least sense in terms of MD's canon, and basically any of the other 3 are just as sensible. Essentially though, the choice at the end of HR doesn't really make a difference since the end result is the same. Go with whichever ending your Adam would align with the most.