It honestly boils down to pettiness.
Guren still plans to bring back humanity through any means, getting Ferid's help to do so.
Shinoa plans to get Yu back even if it mean killing Mika.
Yu & Mika changed their goal from bringing back humanity to bringing back angels & humanity.
Saito & the high ranking vampires want to stop the first.
The reason I say petty is because Saito wants to stop the first even though it benefits him.
Shinoa wants to get Yu back but he ain't going to sacrifice Mika to do so anyway.
Guren is betraying the ppl who helped him once again.
I hope this helps, I myself am confused but tried my best lol. I skimmed after 27 since I'm waiting for the physical copy.
I'm sorry, but I'm totally lost. What's is going on now? Who serves who? What purpose are they fighting for now? Who's good & bad? And many more questions ..... My brain is fried right now (@~@)