Agents Of S.H.I.E.L.D: 19 Easter Eggs, In-Jokes And References In Season 2
The MCU tie-ins you expect. A Sonic the Hedgehog burn? Not so much.
Agents of S.H.I.E.L.D. season 2 ends with Coulson and Skye jetting off to find and recruit others with special abilities, in order to help them harness their abilities and make sure theyre used for good. As seen on the file he hands to her, the codename of this project is Caterpillars.
In the comics, Caterpillars is a codename given to the Secret Warriors, three teams of agents with special powers put together by Nick Fury, and one of which is led by Daisy Johnson. The purpose is due to many agents being compromised, thus necessitating the need for a team no one knows about.
It looks here as though itll be Coulson taking on the Fury role, but Daisy/Skye will be fulfilling much of the same purpose, and indeed the show have now already started teasing the Secret Warriors for season 3 in their promotional images.