In the Community episode "Remedial Chaos Theory", it's clear that the happiest (and principal) timeline is the one where Jeff leaves and the group can be free from his judgment. That makes me think of why the darkest timeline is the one where Troy leaves. Is this saying something about Troy's personality in relation to the group (like in the principal timeline)?
The individual hypothetical "what if"s if a member of the group leaves the group are what Abed thinks will happen.
Since Troy is Abed's best friend, it's how Abed perceives everything is going to be if Troy leaves.
It has also been mentioned by critics that this means that Troy is essentially the glue of the group without which the group will descend into chaos