I just finished fallout 3 goty edition.

my favorite DLC is broken steel and point lookout.

but, my most hate DLC is mothership zeta.

not because i'm fallout really devoted fan, but because it is plot hole.

i don't think alien start the great war. this is stupid idea.

i feel it is fan service joke DLC.

is mothership zeta is non-canon, or canon?

No, it's not canon with previous Fallouts, but the developers of games create canon as they go. For example, the GECK in Fallout 2 wasn't canon with Fallout 1.

Stuff changes. Read through the various DnD rules sometime.

For that matter, the world isn't canon.

"Dammit, where did all these countries in Eastern Europe come from? When I was a kid, you just said Soviet Union and were done with it!

"

This.
Furthermore, no offence but.. just because you think it's a "stupid idea" (I do too, actually), that doesn't make it non-canon.

I think the whole "aliens started the great war" thing gets thrown around too much. I don't think they do, even in Zeta. They don't actually specify when they probed the guy for the launch codes, and given their modus operandi, it seems pretty likely they just wanted it for archival purposes, and they don't like their prisoners trying to withhold information, as strategically irrelevant as it may be.

As for canon, it doesn't really matter, since we probably won't see it again. It might be brought up as an easter egg in a future game, but nothing beyond that.

I've always thought it was an overreaction. To me it seemed the aliens don't understand human speech any more than we do theirs.