The Escape from New York City was the final confrontation of Syphon Filter 2. It involved Gabe Logan and Teresa Lipan attempting to flee from the Agency, as well as NYPD SWAT teams called in to stop them. Conflict between the antagonists generally had them gang up on Logan and Lipan - but there were instances where Agency snipers had pinned down law enforcement, and Gabe was in turn required to cover the SWAT personnel.

While Gabe was mostly successful in his endeavours, curing Lian Xing of Syphon Filter, Teresa Lipan was shot and assumed killed in action. The Agency was presumed to have disintegrated with the deaths of Jason Chance, Archer and the leader, Lyle Stevens - but Vince Hadden decided to use Logan and his companions as a scapegoat for the Black Baton assault on Washington DC as well as the shootings carried out on the streets of New York.




With the Agency disbanded, Vince Hadden over-ambitiously attempts to charge Gabe and his team members with the crimes of perpetrating the Washington DC Attack and the murder of various SWAT members, despite the US administration having fallen allowing him to have the power. He calls off an attempt to kill Logan and his followers while they grieve the apparent loss of Teresa Lipan, who was in fact still alive but in recovery.