In flashback, we see a young Lex at the Excelsior Academy - Lionel comes to visit Lex who is out on a ledge claiming to be protecting his brother Julian. Lex is singing to a bundle and goes out on the edge – the bundle goes flying as Lex wakes up from where he is standing on a ledge as Lana pulls him back. When she goes to tell Clark he explains about Julian and goes to talk to Lex. Lex dismisses Clark's concerns and goes to visit Dr. Garner of the Sommerholt Institute and Clark secretly follows. Garner uses an experimental treatment to awaken Lex's lost memories and we see Lex's unattended 12th birthday party, where Lionel gave him the lead box he later gave to Clark.
Clark confronts Lex – when that doesn't work he goes to Lionel who doesn't seem concerned about Lex's missing memories and accuses Clark of not wanting Lex to regain his memories either (showing him the asylum tape). Lionel then goes to Lex and advises him to stop, triggering another flashback – Lex spying on his parents as Lillian reluctantly bonds over infant Julian despite her reservations about Lionel and his treatment of Lex. And then there's another flashback/memory of Lex apparently smothering Julian in his sleep.
Lionel comes to visit Clark and Martha and asks Clark to help him with Lex, who is supposedly accelerating the treatments. Clark confronts Garner, who is weakened by the kryptonite-augmented treatments – it's a set-up by Lionel, who is giving Clark to Garner in return for Garner discontinuing Lex's treatments. When Lex finds out his treatments have been cancelled, he lies and tells Lionel he's recovered his memories, provoking Lionel to confront him. Garner goes on with the treatments, probing Clark's memories.
In flashback we see two people, Jor-El and Lara, putting a baby Clark into a spaceship and sending him off. Then the system overloads, triggering an alarm and raising Lex's suspicions. He goes in and finds Garner in a coma, the facility in ruins, and Clark unconscious. Later Clark and Lex talk but Lex doesn't reveal his responsibility in Julian's death. And then Lex has another flashback, where he finally remembers seeing his disturbed mother smothering Julian, then taking the blame to protect her. Lex confronts Lionel again and tells him what he remembers - reluctantly Lionel believes him and regrets everything that might have been different. And Martha and Clark bond over his newfound knowledge of his biological mother.