While leaving San Francisco on a train, the CIA capture Alice Monroe (Daryl Hannah) and hit Nick with a tranquiliser dart. He falls from the train doors while crossing a bridge into the water below, but survives.
He sends a video to the CIA Headquarters to blackmail them first into giving up Alice, and then phones up to seal the deal - and exchange him for her. He is disguised on a street outside using the payphone, and while on the way out the CIA boss (Stephen Tobolowsky) shuts down the whole project, but Jenkins and his team go rogue.
They throw Alice into the first taxi they see and then chase after Nick - only to find that it is his little friend who owns the beach house. Nick reveals himself to Alice disguised as an Asian taxi driver - but soon the CIA have choppers in the sky and force them to crash. Jenkins chases Nick's levitated head through the streets, as he takes off his visible clothes and washes the make-up off his face - but then ends up on a building site and gets his little suit covered in dust.
Taking a service elevator to the top, they exchange a bit of negotiating - with Nick on a walkway above a large drop holding his dusty suit jacket out to the side. He goes through a fake "I'm sick of the game" type routine, and as he moves the jacket back pretending to jump, Jenkins reaches out but loses his balance - and falls to his death.
Alice is distraught, but told to forget she was ever there by Tobolowsky as the case is closed - until Nick arrives by her side silently to comfort her and they make a quick getaway.
As it ends, it seems they live happily-ever-after in Switzerland enjoying the ski, and as Alice brings him a cup of hot chocolate, we see that they are going to have invisible little Nick and Alice's running around soon.