It's tough out there for a spy. Just when Bobbi has completed her mission and done everything needed to support "the real" S.H.I.E.L.D., she sees how far they are willing to go to stop anyone in their way — including ignoring her orders and killing Skye. With Bobbi and Mack's betrayal on Agents of S.H.I.E.L.D. complete, everyone has to choose sides. While Bobbi obviously has strong loyalties to Agent Gonzales, I think her feelings for the team may make Bobbi rethink her alliances and possibly even lead her to helping Coulson. In an interview with Entertainment Weekly, Adrianne Palicki (who plays Bobbi Morse) dropped these Agents of S.H.I.E.L.D. spoilers regarding her conflicting feelings for how they are handling the S.H.I.E.L.D. takeover.
She cares about these people. That’s where the struggle comes from. She’s really struggling with the balance of, 'What is the right thing?' She started off knowing what the right thing was, but now she’s going to start having the struggle of, 'OK, you guys have to understand. I know Skye. You guys don’t know Skye like I know Skye. She’s not a bad person. She’s a SHIELD agent first.' It’s going to be a lot of those moments where she’s trying to convince people who just don’t want to hear it.
Clearly, she hasn't forgotten about all of the solid bonding that went on in the bus. Beyond getting back together with Hunter, she was actually friends with these people. She fought beside them and grieved with them when Tripp died. New S.H.I.E.L.D. obviously doesn't hold her team in very high regard, seeing as they are working to eliminate them. Sidenote: I hope Director Gonzales comes up with a new name for his organization, this New S.H.I.E.L.D./Real S.H.I.E.L.D. business is confusing. Life was so much simpler when the enemy was just Hydra.
This conflict of interest for Bobbi might just cause her rethink her alliance with New S.H.I.E.L.D. Even if she didn't always agree with Coulson, she understood that he was working for the greater good and trying to protect the team. If she cannot convince everyone on the other side to listen and give Coulson's team a chance, she might have no choice but to get back into contact with Coulson or May (well, probably not May) to try and warn them of the danger they're in. She might even become a triple agent. Obviously she'd be more than capable of that.
I'm not sure if Bobbi would totally shake her loyalty to Agent Gonzales that easily, but if she did, it would be pretty cool to watch her juggle all of those different super-spy angels. Imagine the intrigue of trying to hide her alliance from Mack, who clearly knows most of her tricks. In an ideal world, Bobbi's understanding of Skye and the team would lead to her convincing New S.H.I.E.L.D. to combine forces and work together.
Maybe that's a little too optimistic to hope for, but if everyone could just work together and get along, they could tackle the real enemy and work on cutting the remaining Hydra heads off. Priorities, people.