A very beat up Will is strapped to a chair and interrogated by Sark. He wants to know what Will can tell him about the 'circumference'. Will claims he knows nothing. The Dentist that tortured Sydney in the first episode walks into the room and says "hello".
Francie tells Sydney that she is going to open a restaurant when she graduates. Sydney gets a phone call from Sark and learns that Sark has Will and he intends to kill him unless Sydney gets the Rambaldi page that was stolen and the ampoule so that they can read it.
Sydney asks Jack to help. He explains that they need to go about this carefully, strategically. He agrees to help her. She needs to steal the page from SD-6, and he will steal the ampoule from the CIA. He tells her not to say a word to Vaughn until they uncover the CIA mole.
Sydney and Vaughn speak, but he senses that she is not telling him something. He comments to Weiss, who in turn asks if Vaughn trusts Sydney. He thinks Vaughn should voice his concerns to Devlin. Later, Devlin, Weiss, and Haladki question Vaughn. They want to know if the Bristows are to be trusted. Later still, Jack calls Devlin. Devlin says he thinks Jack is the mole but Jack asks if they are friends. Devlin says yes. Jack hangs up and then kidnaps Haladki. After serious interrogation it turns out that Haladki is the CIA mole and has been working for Khasinau. He tells Jack what he knows about the circumference. There is a gunshot, and it seems Jack kills Haladki but it's not known for sure.
Sloane takes Emily to a beach house and tells her the truth about SD-6. Later, Sloane meets with the Alliance and they grant him a place within the inner circle but it's contingent on him killing his wife. Later still, Sloane puts some sort of drug into Emily's wine. She drinks, but her fate is not known.
Dixon follows Sydney. Sydney swims to the SD-6 compound and steals the Rambaldi page. When she gets out of the water, Dixon is waiting for her. He wants to know who she is working for. She tells him that he needs to trust her. She says it's classified but he threatens to report her.
Abby gives Will's editor his story, and she wants to publish it.
Will is tortured, his teeth are pulled, and he's injected with truth serum, but he knows nothing - so Sark's men prepare him for the exchange. Before the guards can take him to be exchanged for the Rambaldi information, Will attacks the Dentist and stabs him. The Dentist survives but Will has some fight in him!
Jack meets with Sark in the Taipei alley. He gives him the Rambaldi circumference information and Sark gives him Will. Instead of incurring Will's wrath, Jack gets a hug and a thank you.
In the Taipei lab, Sydney destroys the circumference but in doing so, releases tons and tons of water. She and Vaughn run but only Sydney gets through the door. Vaughn is seen, underwater, through the window. Sydney tries to break it but can't.
She is knocked out and when she awakes, Khasinau is there. She says she has questions for him and he says she can ask his boss. She says she thought "The Man" was the boss and he says yes, but he is not "The Man". After he leaves, a woman walks in the room and says, "I've waited almost thirty years for this" and Sydney says, "Mom?"