The episode began with a trucker barreling down the street, singing along with his radio, when he gets a call. He tells the person on the other end of the CB that the cargo is secure, and is almost immediately motioned to turn over by someone in a black, official-looking SUV. When it pulls out in front of him, it flips over and he starts to freak out, at which point you see that his truck has the SHIELD tech in it and he's trying to figure out what's attacking all the vehicles around him, throwing them in the air and crushing them. Then, they do it to his truck and while he's in the air, he calls in but is dropped before he ever gets to explain what's happening and crashes.
On the side of the road, a number of soldiers with a construction crane break into the back of the truck, cut into a SHIELD vault with torches and take a man, who is strapped into a metal seat and asks "Are we there yet?"
Cut to the bus, where Ward is training Skye in basic boxing skills. She's annoyed about having to do all the physical labor, but Fitz and Simmons explain what the training is like to be a non-field agent (lots of science stuff) and she gets back to it. She asks him what his moment of truth was that got him to decide he was right for the job.
Ward tells her that the truth serum he was given in the pilot was BS and that he had only given her a "priority one overshare" to con her into helping.
In the conference room, Coulson tells the group that Dr. Franklin Hall had been abducted by invisible enemies. He's one of a few select scientists SHIELD has been protecting.
In the field, the truck driver says that he's convinced the bad guys are working with someone within SHIELD. Fitz and Simmons find a small electronic device that's conducting an electromagnetic field, kicking up debris, and deactivate it. Coulson picks it up and says that it's "something big."
Back in the lab, Coulson tells Melinda May about the mole theory. Ward found a tire tread pattern and came up with three suspects who may have sold the construction equipment to the kidnappers.
Skye asks Coulson about the truth serum and he evades the question, walking away, while Melinda comes in and gives her a mountain of paperwork to read through to look for evidence of a mole.
Out in the field, Coulson approaches a man on horseback and asks him who paid him. The man pulls a shotgun on Coulson, but is knocked off the horse by Ward. He says it was given to him anonymously in gold, so Coulson confiscates the gold to investigate. They look into it, figuring out it's from a Tanzanian mine owned by Ian Quinn.
In his own lab, Quinn has Hall, who accuses him of plagiarizing Hall's work in the past. Quinn said that he was "rescuing" Hall, who says he's impressed that Malta is his hideout since SHIELD has no authority there.
Quinn says, more importantly, they can't touch Hall either. he shows Hall one of the devices--"a theoretical machine powered by a theoretical substance" called Gravitonium. It's one of the machines SHIELD just got their hands on in the field and Fitz and Simmons are looking into it while Skye looks on.
Skye is hard-pressed to believe that Quinn would do anything bad, saying that he's a great guy who gives lots to charity. Back at Quinn's lab, though, he shows Hall a ten-foot-tall version of the little machine, telling him he needs his help to make the machine stable.
Ward figures out that there needs to be a big strikeforce, but that such a force would break laws. Skye figures out a way to get herself an e-vite to a stockholder's meeting at Quinn's lab while playing on her smartphone.
Coulson tells Ward that while he understands his concern, there's not a lot to be done about sending Skye in. He objects about sending her on a covert op, that he doesn't trust her and he's worried about both her safety and her loyalty. Coulson tells Ward that he has to start talking to her like a person. During their next workout session, he gets all emotional and tells her that when he was a kid, he had a brother who used to abuse him and his younger brother, and that was his "moment" that she had asked about.
In the ocnference room, they give Skye a whole rundown of the plan, including a compact that will give her covert wireless access to Quinns computers.
May objects to Coulson going in with Ward, saying that he's not combat ready. He counters that he's had plenty of action with The Avengers and she counters that he died doing it.
At the Quinn compound, Skye is having some fun at a party, using SHIELD's comms to get around people. Quinn offers her a job almost immediately, asking her if she wants to come work for him in risk analysis.
Leaving her to consider it, he goes and make sa keynote speech in which he singles out a number of institutions including SHIELD that he's opposed to, and he drops the announcement about Gravitonium.
On the beach, Coulson and Ward are discussing the extraction while inside Skye is trying to get access to rooms where she can try to get online. Quinn catches her, asks her what she's doing and in the way of trying to get herself out of it, she writes on a piece of paper "SHIELD is listening" and shows it to him.
Back at the lab, Melinda May, Fitz and Simmons are listening in, trying to get into his computers, until the earpiece cut out. At Quinn's place, Skye is sweet-talking him, using the fact that she broke contact with SHIELD as a signal she's trustworthy.
In Quinn's office, he tries to convince Skye that SHIELD is using her because she's a genuine threat while Ward and Coulson fight off Quinn's security guards.
Coulson finds Hall and tries to rescue him, but Hall doesn't want rescue--he wants to destroy the machine Quinn created based on his work--and Quinn with it. Hall, it turns out, was the leak that told Quinn how to find Hall--so that he could gain access to, and destroy, the device.
Meanwhile, Quinn destroys the compact and levels a gun on Skye.
In the lab at Quinn's compound, Coulson wakes up and calls in to the lab on the bus. Quinn says he's protecting all mankind, and pours himself a drink in a room that's spinning; while he and Coulson remain oriented the whole time,
Quinn, with a gun to Skye's head, calls SHIELD "big brother," and she tells him (via a bastardized version of Ward's story) that they're the "good" big brother. She disarms him, taking his gun using methods that Ward taught her and then jumping off the balcony into the pool. Finally, Quinn figures out what's going on with Hall and decides to evacuate.
Coulson tells Hall that Fitz and Simmons, his former students, are in his ear right now and tells him that they could have worked with him. He says SHIELD is just as bad as Quinn--that the invasion in The Avengers happened because they were messing with the Tesseract.
Outside, the chopper takes off and Ward catches up with Skye. Hall believes his actions here, killing hte people on the island, will save millions. Having been told that they needed a catalyst to create a chemical reaction in the middle of the Gravitonium in order to stop it, he throws Hall into the middle of it, apparently killing him.
He calls down to storage, telling the agent storing the device that it has to be buried deep, never cataloged or identified, or it's that guy's job--that's what Hall would have wanted.
May tells Coulson--who is struggling with his gun for the second time in the episode, saying that he's having trouble with what should be muscle memory--that she wants in for combat next time around.
Punching the bag when Ward shows up, Skye has a moment with Ward, talking about their shared past as troubled youths in foster families. She's committed to SHIELD, now, and returns to the punching bag, telling Ward that she knows there's a truth serum.
The PS, as you might expect, involved the Gravitonium being shunted to the vault, only to see a hand-shape coming out of it.