Episode Summary from en.wikipedia.org:

Ward, Fitz, Simmons, and Skye go to a S.H.I.E.L.D. Academy to investigate an attack upon students, which was done with an "ice machine", a device that can freeze people and their surroundings. During their time there, another ice machine goes off, freezing cadet Donnie Gill (Dylan Minnette), though the agents are able to save him, and Fitz later gets to know Donnie, seeing much of himself in him, and helping him solve an problem with a new power source Donnie has invented. The team learns that Donnie and his fellow cadet Seth Dormer (Daniel Zovatto) are behind the ice machines, and that the power source Fitz helped him perfect was for a larger version of it. Meanwhile, Coulson and May head to Mexico City to find a former agent named Richard Lumley (Boyd Kestner), who tells them of a mission 24 years earlier involving an 0-8-4, which turned out to be Skye. He warns them that she is dangerous, as many agents, including his partner, Linda Avery, died trying to protect her. After meeting with the rest of the team, Coulson relates what Lumley revealed to Skye, who is devastated at the revelation. Donnie and Seth activate the larger device, causing a huge ice storm that Seth hopes will impress Ian Quinn, for whom Seth's father works as a lawyer at Quinn Worldwide. Realizing his mistake, Donnie attempts to shut it down, but a bolt of lightning destroys the machine and puts Seth in cardiac arrest. May tells Coulson about her sexual relationship with Ward; Coulson says he trusts her to comport herself responsibly, but adds that, if it becomes a problem...to which she responds she will break it off. The team apprehends Donnie but is unable to save Seth's life. On his way to the Sandbox for observation, Donnie realizes that the explosion of the ice machine has given him cryogenic abilities. In the final scene, Ian Quinn receives a call from Coulson warning him that if his aircraft flies over any country that is a S.H.I.E.L.D. ally, it will be shot down. Before hanging up, Quinn gives Coulson a message that the Clairvoyant says hello.

Episode Recap from abc.go.com:

A few cadets at S.H.I.E.L.D. Academy blow off a little steam by taking a dip in the pool. Their swim is cut short when ice begins to form on the surface of the water. One cadet, Seth Dormer, gets his leg caught until another young man, Donnie Gill, is able to break him free. The team learns that a device had been placed inside the pool causing it to freeze. The headmaster, Agent Weaver, is worried there’s a bad seed at the academy.

Skye is impressed by the academy’s Wall of Valor which pays tribute to agents lost in the line of duty. She’s also envious, as she wishes she was deserving of such honor. Ward assures her that all she needs to join this particular club is a dedication to the greater good. He then interviews Seth Dormer. The kid says that the cadet who helped free him, Donnie Gill, has trouble communicating with those less intelligent than him. Donnie is front and center in the auditorium as Fitz and Simmons give a lecture. He rises from his chair in a panic as ice forms all over his body. Moments later, he’s frozen solid.

Fitz and Simmons race to save Donnie. Ward smashes the device that’s doing this to him. This frees Donnie. It looks like he was the intended target at the pool. Agent Weaver says Donnie has had trouble adjusting at the school. Fitz bonds with the kid. He’s very impressed at his big ideas. He even helps the cadet figure out the solution to a project that’s perplexed him.

Simmons, Skye and Ward hit an underground student hangout known as the Boiler Room. That’s because it actually is a boiler room. A really cool one. Callie Hannigan is there. She’s an ambitious cadet who was also at the pool. She says that Seth and Donnie have been talking about meeting Fitz for weeks. This was all a setup to get the team there. Fitz unwittingly helped figure out a way to power a bigger version of the ice machine. Seth renders him unconscious as he and Donnie escape with their dangerous device.

Coulson is still coming to terms with the truth he recently learned about his death and revival. May flies him to Mexico City to get his mind off things. They are tracking down the partner of the agent that dropped off Skye at the orphanage. His name is Richard Lumley. The guy has been spotted after 23 years off the grid. May wants to find Lumley before he disappears again. During their initial stakeout, she assures Coulson that she knows him well. S.H.I.E.L.D. may have changed his memories, but they didn’t change him. May also admits that she and Ward have been having sex. That tidbit gets put on hold once Coulson spots Lumley.

Despite his best efforts to get away, Lumley has nowhere to run when Coulson corners him on a fire escape while sitting in a hovering Lola. He knows this is about the baby girl. His partner died after getting involved in a mission involving an 0-8-4, an object of unknown origin. An entire village had perished trying to protect this one. The 0-8-4 he speaks of was the baby girl. He and his partner knew they had to erase themselves and the baby from existence. They knew that whoever killed the village and many other agents was a force to be reckoned with.

Coulson and May meet up with the rest of the team to deal with the crisis at the academy. Fitz realizes the cadets have a financial backer. This would be Ian Quinn. The sleazy money man is buying their technology. The cadets have no idea Quinn is a criminal as he asks for a demonstration of their product. The boys set up their machine. Donnie thinks using the device is unsafe. He doesn’t want to do it, but Seth convinces him to stick with the plan. Donnie fires up the machine.

Coulson lets Skye in on what he learned in Mexico. It’s extremely hard for her to hear. Down on the ground, Donnie’s machine causes dangerously large ice balls to fall from the sky. It’s just the beginning. Donnie has created a super storm. May flies the bus into the eye of the storm where Seth has been knocked unconscious. The bus hovers over the boys. The team brings them onboard where Simmons is unable to revive Seth. Donnie is devastated.

The super storm subsides. Donnie is transported to the Sandbox, but not as a researcher. They want to keep an eye on him. After he’s gone, Coulson lets May know that he told Skye the truth. Her world was shattered. Or so he thought. Coulson reveals that Skye didn’t see it that way. She thought she wasn’t wanted her entire life, but all this time it was S.H.I.E.L.D. protecting her. It’s this outlook that restored some of Coulson’s faith in humanity. It’s up to us who we become. This is true for Donnie, too, as he seems to now have the power to turn things to ice. As for his backer, Ian Quinn, he lets Coulson know that he’s associated with the Clairvoyant.

Please use this thread to discuss the series' twelfth overall and first season twelfth episode Seeds. Rule: Please keep spoilers limited to those revealed during the series up to this episode only.