Agents Of SHIELD Season 3: Everything We Know So Far
2. Secret Warriors
For Skye and Coulson, season 2 ended with the pair going off together on the search for more Inhumans, putting together a team that has to remain anonymous, with a file seen labelled 'Caterpillars'. That was a pretty big tease for what's to come, as it leads to the comics storyline of Secret Warriors.
Daisy Johnson is a big part of that, leading one of the teams, which consist of super powered agents working in, you guessed it, secret. Although there are three teams in the comic, S.H.I.E.L.D. will presumably just be focussing on the one led by Daisy, with Coulson filling in the Nick Fury role of being the man who organises everything.
It's a safe bet that Lincoln/Sparkplug will be part of the team, but also means that we should be meeting a few new Inhumans as well. Daisy's team consists of the likes of Phobos, who has super strength, and fear-inducing abilities; Yo-Yo Rodriguez, capable of running at super speeds; and Hellfire, who can produce fire and attack people with it. It's not difficult to imagine these appearing on the show at some point, and the Secret Warriors story should run throughout the season, and be part of the tie-in with Civil War.