'Agents Of S.H.I.E.L.D.' Theory: Mack & Bobbi Are Working For Tony Stark, Because The Clues Are Undeniable
You can always count on a covert non-government agency to have plots hidden within plots, or at least you can on Agents of S.H.I.E.L.D. From the moment Bobbi Morse joined Mack on the S.H.I.E.L.D bus it was clear that they had an agenda they were keeping from Coulson and his team. Now that we know for sure that they aren't Hydra, the solution is pretty clear: Mack and Bobbi have abandoned S.H.I.E.L.D and are now working for the erstwhile Iron Man at Stark Enterprises.
I think that, like Agent Maria Hill, they joined Stark after Hydra infiltrated S.H.I.E.L.D to avoid being killed by double agents, and to gain Stark's fleet of lawyers to protect them from the U.S. government who were gunning hard for all S.H.I.E.L.D. operatives. Once they started working for Tony Stark, they were given orders to track down Nick Fury's famous "toolbox," and bring it back to headquarters so that Stark could see what it is made of. It makes good spy-sense to pair these two up for this mission. Mack can clearly handle technology side of things, be it human or alien, and Bobbi can beat up anyone who stands in their way.
Once Bobbi and Mack got wind that Coulson was rebuilding S.H.I.E.L.D from the ground up, they probably figured that Fury must have left him the toolbox, and infiltrated the team to get closer to it. Now they just need to wait for the right moment to steal it from from Coulson's office and get out of town without anyone noticing they knocked Hunter unconscious. OK, that one might take some serious strategy, but it's not like there aren't plenty of other distractions on the bus.
This development could also lend itself nicely to an Agent Carter crossover, assuming (fingers crossed) it get's picked up for another season. Perhaps the toolbox was another one of Howard Stark's inventions that he gave to Peggy Carter as a gift when she started building S.H.I.E.L.D. Tony Stark may very well recognize his father's handiwork and want to take a closer look. Or it could have been another piece of confiscated goods the Howling Commandos acquired after the (first) fall of Hydra. Either way, it leaves a nice opening for us to see Hayley Atwell on screen again.
If my theory is correct, it is hard to tell what impact this development would have on Tony Stark, and by extension the rest of the Avengers team. Assuming Bobbi and Mack are working for Stark Enterprises, it seems like a huge stretch that the truth about Coulson's death and resurrection wouldn't spread. While I highly doubt they would do an Avengers/Agents of S.H.I.E.L.D crossover to address this, a girl can dream.
No matter the reason for Mack and Bobbi double-crossing the team, the results are bound to be explosive. We've already had our hearts ripped out once with back-stabbing on S.H.I.E.L.D., and the team is still reeling after the sudden loss of Tripp. I do not see anyone handling more betray well.