When a piece of tech invented by Fitz (Iain De Caestecker) and Simmons (Elizabeth Henstridge) is used in the attempted murder of three S.H.I.E.L.D. cadets the team heads to the the science and technology division of the S.H.I.E.L.D. Academy. As Ward (Brett Dalton) begins his investigation, Fitz and Simmons give the students “the talk” (about the history of S.H.I.E.L.D. and the dangers of those using science for evil) which is interupted by a second attack on a genius outsider named Donnie Gill (Dylan Minnette) who has had trouble fitting in during his short stay at the Academy.
With the rest of the team busy at the Academy, Coulson (Clark Gregg) and May (Ming-Na Wen) head out on their own mission in Mexico fueled by Coulson sharing the truth about his experiences under Centipede with his most trusted agent and a lead in the investigation of Skye‘s (Chloe Bennet) past involving the long lost partner of the woman who dropped her off at an orphanage. Former Agent Lumley (Boyd Kestner) knows enough of Skye’s history to raise the hairs on Coulson’s neck. Despite May’s warnings, Coulson chooses to tell Skye the complete truth about her past and the number of S.H.I.E.L.D. agents who died to keep her secret safe.
Some well-spent time in the student’s unofficial union, and at talk with an ambitious student (Maiara Walsh), gets Ward the information on true identity of the people responsible for the attacks and the reasons for their creation. However, by the time they’ve learned the truth Fitz has accidentally helped the pair fix the ice weapon Ian Quinn (David Conrad) planned to pay the two cadets (Minnette, Daniel Zovatto) handsomely for. Flying the S.H.I.E.L.D. bomber into the eye of the out-of-control super storm released by the device, May and the team are able to rescue Donnie who is sent away to the Sandbox (but not before being changed by the experience).
“Seeds” offers the origin of another super-villain to be used somewhere down the line but the episode’s more lasting effects are the choice of the writers to make Skye an 0-8-4 whose true origins are shrouded in death and further mystery. It opens up nearly infinite choices for her true origins, not to mention what she might be capable of, while still offering a positive spin on the bad news by Skye using the knowledge to move forward thankful for what S.H.I.E.L.D. has done to protect her for years which also helps Coulson heal from the wounds uncovered concerning his own recent past.