Helps aswell that Leviathan and From Ashes help smooth things in the lead up...
Hell I remember one conversation with Shepard and Javik that felt like it should've been in the base game
To abbreviate it went something like this...
"Hey this Cerberus conflict is pretty arbitrary isn't?"
"Well they used this same tactic back in the Prothan era, and turned our own people against us."
"I guess that makes sense then."
(There's a lot more then just that Javik clears up but you get my point)
It also helps as well when Leviathan doesn't really know what to make of Shepard neither do the Reapers and when you reach the Catalyst it makes sense that it's reaction is just
"I dunno, do what you'd like I guess, didn't expect you to actually make it this far..."