First of all sorry, because there may be some grammatical (or of other nature) errors... I'm not English and I don't speak from a few years the language (using Google for a few things).
I have another option... is it possible that Ein killed Zwei?
I mean, the meaning of all is that they are killers and now it's time to "rest". We know that...
1) Ein was considered dead (not sure about this, Scythe Master entered in Inferno after she escaped) from the organization after Zwei shooted her (but she is still alive), so it is possible that they do not know it (again, not sure about this), so it would be explained, BUT if I was a killer I'd shoot both, because it was clear they were travelling together and would not leave alive a possible witness.
And, the organization, knowing that they had to kil one (or two) special assassin(s), why sending only one who shot with a silencer in a wasteland.
2) A few times Ein scold Zwei not to be a good liar like she is: she knows that Zwei will live in guilt for killing Drei (although he said the opposite) and, to relieve his pain, shows him her true smile, like a sort of reward for not making him suffer anymore, since when he saw her smiling, smiled too (a true moment of happiness): then she kills herself by eating a poisonous flower.
Now maybe is going to be easier than I thought, but I would not leave this option.
