“Afterlife” is episode sixteen of season two of Marvel’s Agents of S.H.I.E.L.D.
In the previous episode, “One Door Closes”, Coulson had escaped when Gonzales’s version of S.H.I.E.L.D. took over the facility, and has met up with Hunter. They go to Skye’s cabin to find her, but discover she has left – the eyeless teleporter Gordon took her away, at her request, when the other S.H.I.E.L.D. attacked; despite Bobbi’s efforts, they were hostile towards her. In fact, Coulson’s willingness to use powered people like Skye is a major factor in why the other S.H.I.E.L.D. doesn’t trust him.
Skye is now at an unknown location where apparently other similar people with powers are taken – taken in a friendly sense, to help them, and be with others of their kind. Only Gordon apparently knows where it is, but the residents call it ‘Afterlife’. Her father and Raina are there too.
The infighting continues at S.H.I.E.L.D. as both Gonzales and Coulson believe they represent the true S.H.I.E.L.D. Gonzales wants Fury’s “toolbox” opened, but Coulson is apparently the only one who can open it.