What did really happen in the end of Phantom: Requiem for the Phantom? Some people claim that those Mongolian flowers are poisonous and that Ein ate one when Zwei died, but I've researched and there is no reliable source that tells us that those flowers are really poisonous. Some people claim that actually, they weren't together, Zwei was somewhere else, and others claim that Ein killed Zwei. 

Did both Ein and Zwei die? What did really happen there?
The anime ending is different from the visual novel.
Ein and Zwei were definitely together in that last scene because Ein was talking to him.   

The poisonous flower idea is a fan theory without official source. There are no official explanations of what happened in the last scene. It does make sense, though, to assume Ein committed suicide after Zwei got shot, and the flowers are the best and easiest tools for her suicide.    

Since there's no official explanation, you can go with whatever idea you want.