Season 6 begins in a downbeat way as Michael pursues Anson and Fi is perp walked and then interrogated by Jason Bly who mysteriously wants Fi to name Michael as the mastermind behind the bombing.

Michael is also angry with Sam, having figured out that he let Fi turn herself in. Sam points out Michael was commiting treason and on the verge of getting people killed but Michael thinks they could have found a way to stop Anson and save Fi.

They track Anson to an abandoned chemical plant but Anson knows they are coming because Michael had used a truck to create a large roadblock (albeit a non-lethal one). Michael manages to get to Anson and punches him and then prepares to shoot but unfortunately Anson had enough time to rig a bomb in the plant (Pearce, Sam and a few personnel are still inside) and Anson has a dead man switch.

Michael reluctantly lets Anson leave and then watches as he blows the chemical plant up. There are a few suspenseful moments as he waits for Sam who had stayed inside trying to rescue a worker Anson had tied up.

Meanwhile Fi refuses to crack under pressure from Bly and is taken to prison.