The Joes follow their enemy to Paris and manage to stop them destroying all the city - although quite a large part of it to be honest is now lying in a green dust. Duke hits the killswitch but is taken hostage on the Cobra chopper and taken back to their underwater lair at the North Pole.
He activates the homing beacon on the warhead briefcase, so the good guys know where to find him, as Dennis Quaid makes a recovery to lead his men.
'Heavy Duty' leads an underwater James Bond inspired attack on the base while the main team infiltrate the base. McCullen launches the 3 remaining missiles - one explodes soon after launch, but Ripcord must get into a prototype superjet and intercept one over Moscow, and then a few minutes later over Washington DC.
While in the lab, Duke learns that the evil mad scientist is his old friend Rex - the brother of Ana his sweetheart/nemesis who everyone thought had died in east Africa. He takes off his disguise and we see that its just the young kid off 'Third Rock from the Sun', so it's not too bad. Ana comes to her senses and rescues Duke. They all have a battle and McCullen somehow manages to burn himself before he gives up and does a runner.
Ana comes round and together they chase the bad guys in a stolen sub. Meanwhile Snake Eyes fights with his adopted brother, the Chinese guy in white, and finally wins. The Chinese fella falls into the icy water.
On board their sub, Rex heals McCullen, turning his head to metal, and dons a metal mask himself, giving them both new names ... until they are cornered by the army and simply surrender. Ana is kept in confinement as they study what the doctor did to her, while the bad guy from the Mummy with the irritating whistle has undergone surgery and is now mascarading as the President, who is English for some reason, lounging around in the Oval office.