It had been 7 months since Skye had disappeared, 7 months where they had twisted her reality, 7 months her team had searched before they found her. "We want you to break her. Sever all of the ties that she has…We want the word 'hope' to be out of her vocabulary. If we let her go, she'll stay because she knows there's nowhere to run." Warning: torture/sexual abuse/suicide attempt.

After saving Grant from himself and his family, Phil enrolls Grant in The Academy, S.H.I.E.L.D.'s pre-communications Academy reserved for the teen children of agents and early recruits. There Grant meets Phil's plucky daughter who teaches him that there is something worth fighting for and he finds a family in the form of his ragtag new group of friends.

Sequel to Hope for the Lost; Skye's origins are discovered after she makes a fateful decision to save her fellow agents. She must learn to navigate SHIELD after this revelation and accept being both a child of monsters and men. How will the team react and will her fellow agents accept or reject her?

The team gets a new mission to look into a mysterious compound in Chad, but S.H.I.E.L.D. dictates that they have help with this one. The help comes with an unexpected surprise for Ward. As the team investigates, they get more questions then answers and one of them doesn't get through it unscathed. Not everything is as it seems. Mid season one some vague spoilers.

"She'd been warned that he'd stated the only thing he'd wanted was her, that she was the only good thing he'd had and he destroyed his chance because of his need to follow Garrett." Skye realizes that behind the murderer is someone as lost as she had once been. She decides to stand beside Ward as he begins his walk on the road of redemption. 1x22 Finale Spoilers