After Sayid encounters Michael, the story of how Ben's spy got to the freighter is finally revealed. Back at Locke's camp, Ben sends his daughter, Alex, to a safer place so that she may survive an approaching attack. [Edit]

At his home in the Others' abandoned barracks, John Locke (Terry O'Quinn) hosts a community meeting to explain to the members of his faction what he has learned about the freighter Kahana's mission, where Ben Linus confirms that Michael is his spy. After the meeting ends, Ben urges his daughter Alex (Tania Raymonde) to flee, for her own safety, to the Others' sanctuary at the "Temple." Alex's mother, Danielle Rousseau, agrees, and plans to accompany Alex and her boyfriend Karl (Blake Bashoff) on their journey.

Aboard the Kahana, Sayid Jarrah (Naveen Andrews) confronts Michael about his purpose on the freighter. The episode's narrative then shifts into an extended, uninterrupted flashback, the longest in Lost's history.[5] After escaping from the island, Michael has returned to Manhattan and has become estranged from his son Walt (Malcolm David Kelley) after confessing that he murdered Libby (Cynthia Watros) and Ana Lucia (Michelle Rodriguez). After an unsuccessful suicide attempt, Michael is confronted by Tom (M.C. Gainey), the Other who abducted Walt; Tom explains that the Island will not allow Michael to kill himself. Tom gives Michael a forged passport, identifying him as "Kevin Johnson," and an assignment: he is told to infiltrate the Kahana, owned by entrepreneur Charles Widmore (Alan Dale) (who, according to Tom, faked the Oceanic 815 wreckage that was found in the Sunda Trench), and kill everyone on board. When Michael attempts to detonate the bomb his new employers provide for this purpose, it turns out to be a fake. Ben contacts Michael by radio and explains that the trick was intended to illustrate that the Others do not want Michael to kill any more innocent people the way he killed Libby and Ana Lucia. The flashback ends, and Sayid, appalled that Michael is working for Ben, exposes Michael's duplicity (and true identity) to Gault (Grant Bowler), the captain of the Kahana.

The episode's final scene returns to Rousseau, Alex and Karl. On their way to the Temple, Karl is shot dead by hidden assailants. Rousseau is also shot trying to flee the attackers. Desperate to avoid being shot herself, Alex calls out that she is Ben's daughter. [Edit]