The first season finale of Agents of SHIELD led the team to the discovery of Hydra and the ramifications it entails for the organization.
In an interview, Clark Gregg has previewed what lies ahead for Agent Coulson when the series returns on ABC this fall.
Coulson got to watch himself pre-memory wipe describing why he thought the whole Tahiti Project was a bad idea. He was talking about all the things that were happening to the people they were using on it and why he suggested they can the whole thing - and looked pretty shaken while he was saying it. So I've got to suspect that some of the stuff he saw and some of those patients have some version of the stuff that's going to happen to him. So we go from having no SHIELD at all, with a director on the run, to a tiny Guerrilla SHIELD with Agent Coulson at its head, and maybe not in his own right head. That sounds fun. That sounds like an interesting Season 2.