I had a similar question so I'll just repeat what hbkdx12 said to me.
Cain only shows up if everyone in your squad (Faye, charlie, bo, Rachael and Cain [you don't have to worry about shindo or kurosawa]) has a trust levels that are in the "Very High" portion; basically they all need to have at least 3 full bars of trust. If this happens by the final showdown, Cain will come in through the roof right before the battle starts.
If you get Cain to show up, He will take the shot from the mech to save Faye in which case he along with everyone else survives.
If you don't have your whole squad at very high trust Cain will not show up thus Big Bo will always take the hit from the mech to save faye and consequently will always die regardless of how high his trust is.
If your trust with bo is too low he will carry out the betrayal in which case when you defeat him, Rachael will be the one to take the hit from the mech and die.
So best case scenario, Cain joins the party and everyone lives
Worst case scenario, You kill big bo, Rachael dies from the hit and only faye charlie and Dan survive.
Again, all credit goes to @hbkdx12
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