What happens when S.H.I.E.L.D ceases to exist? Chaos.
Even though Coulson and his team secured the Hub, they weren't safe there. Colonel Glenn Talbot was on his way and ready to interfere with their freedom and search for Hydra on Agents of S.H.I.E.L.D. Season 1 Episode 18.
Unclear on who to trust, the team got on the bus and went rogue.