After extracting an undercover S.H.I.E.L.D. agent and his Level 8 classified intel, Coulson‘s (Clark Gregg) team heads to S.H.I.E.L.D.’s secret information and organizational station known as The Hub. While Fitz (Iain De Caestecker) and Simmons (Elizabeth Henstridge) grab some of S.H.I.E.L.D.’s new technical doohickeys, Coulson, Ward (Brett Dalton), and Melinda May‘s (Ming-Na Wen) are briefed by Victoria Hand (Saffron Burrows) on a group of separatists who plan to use a sonic weapon named the Overkill to forcefully declare their independence from Russia and Georgia. Hand’s plan to stop them calls for a two-man team (the unlikely pairing of Ward and Fitz) to find and disable the device.
Given both she and Simmons are kept out of the loop on the dangerous mission involving their friends, and unable to pry an information out of Coulson, Skye (Chloe Bennet) convinces Simmons to do a little unauthorized snooping which leads to an awkward attempt by Simmons to try and sweet-talk her way out of trouble and then attack Jasper Sitwell (Maximiliano Hernández) when the agent catches her acting odd in a restricted area.
After Skye discovers Hand sent her teammates in on a suicide mission without an extraction neither she nor Coulson are particularly pleased. This leads the remaining members of the team to attempt a four-man off-the-books exfil to save their Fitz and Ward who just need to stay alive long enough for their friends to reach them. The message of “trusting the system” is espoused several times over the course of the episode, but only the team working outside the lines saves their friends’ lives. The sequence of events works well, but the episode ends with S.H.I.E.L.D. looking like a far less trustworthy organization than when it began. And by the end even Coulson’s faith in the system is a little shaken.
The team’s time at The Hub offers a unique situation for first Skye, and later Coulson, to look into her heavily-redacted past. Although Coulson offers her part of the truth, that a S.H.I.E.L.D. agent was responsible for dropping her off at an orphanage, he only shares the full file with May in hopes that the two of them can piece together the story behind the gruesome circumstances he’d like to keep from his new agent-in-training. And the episode also continues Coulson’s own tale of returning to duty different after New York as his response to Hand about Tahiti (the exact same phrase he’s used over and over when asked about his rehab) begins the agent to go down a rabbit hole of his own which leads to the discovery that the full truth has been hidden from him, in much the same way he’s just done with Skye, most likely by Nick Fury (Samuel L. Jackson).