This episode begins at the destruction of the Galley-La offices from Lucci's kick, the Straw hat crew's defeat, and the arrival of the CP-9 to Franky's warehouse.
Zoro is running over the rooftops and is lost. Luffy is heard and seen stuck somewhere. Zoro sees the fire and knows where to go. As he's running a sudden gust of wind blows him off out course.
The scene goes back eight years.
Spandam arrives to arrest Tom.
The opening theme starts.
Spandam takes credit for catching the criminals. The people are suspicious of why Tom would attack the ships when he was being pardoned, but think about how he also made the Pirate King's ship.
Franky accuses Spandam of causing the attack, but he can't tell them the motive. Franky denies the very ships he built. Tom stands and strikes Franky for rejecting the ships he built.
Tom charges Spandam and strikes him so hard that half of his face is permanently damaged. Before he can do more the Marines open fire. He falls to his knees and realizes they were tranquilizers.
Tom accepts blame for the attack, but but requests that the pardon instead be used for his crime today. This means he will be sentenced to death for his involvement in of building the Pirate King's ship. To that crime he is proud of.
The judgment is passed that only Tom will be taken to Enies Lobby. Iceburg and Franky are released.
Franky can't stand watching Spandam kick the unconscious Tom anymore. He rushes, grabs a Marine rifle, and uses to to strike Spandam across the face. Franky tries to defend Tom. He's shot and Iceburg tries to buy Franky time to run.
As the Puffing Tom is transporting Tom to Enies Lobby, Franky climbs on the tracks and fires a cannon at the train. The shells don't stop the train, and Spandam order they run him over. Franky pleads with the train to stop and is run over.
Before the train strikes we see when Tom first met Franky as a small boy.
Back in the current time, the CP-9 question Franky about the past. He was thought dead and his crimes were dropped, but now that he is alive. Lucci plans to take him to Enies Lobby. This could be changed if he hands over the blue prints.
Blueno connects via a Den Den Mushi to their superior. The one now in charge of the CP-9 is Spandam. He is speaking from Enies Lobby, but wont be fully scene in more detail until episode 263.
During the wide shot of the warehouse just before the finale, Kiwi and Mozu are nowhere to be seen.