"These relationships are not fixed. There are no guarantees about any of these characters. Just because characters are allies now, doesn't mean they're going to remain allies."
And Nolan says that outside forces are going to put pressure on Carter regarding her relationship with Reese:
"One of the fun dilemmas of our show is you have these people doing the right thing, but in unorthodox terms and illegal terms. There are influences within her office, or various other law enforcement agencies, that are going to start to inquire as to what she knows. What sort of position [does] that put her in?"
Do you like that Carter is now working with Reese and Finch?
Source: TV Guide