The game's prologue mission starts in Paris, France, with James Bond helping French Intelligence operative Dominique Paradis evade a gang chase while chasing a truck with a stolen nuclear weapon, before continuing in his car. After stopping the truck from blowing up the Eiffel Tower, Dominique and James celebrate New Year's Eve.

The British Government sends Bond undercover to a party in industrialist Raphael Drake's Austrian castle. M believes that the party is a cover for the exchange of a missile guidance chip between Raphael Drake and Alexander Mayhew, who manages the Japanese branch of Drake's industry, Phoenix International, and had stolen the chip from the United States. Phoenix is believed to be a front for weapon smuggling. M gives Bond the instruction for 007 to rendezvous with CIA agent Zoe Nightshade and Dominique, who is posing as Drake's mistress. While Zoe distracts the guards, Bond makes his way to the exchange and steals the chip. Agents Nightshade and 007 make an try to make an escape on a cable car, when Drake's bodyguard, Rook, attacks the cable car with a rocket-launching helicopter. Bond shoots down the attacking helicopter using rockets found in the cable car. James and Zoe then escape Drake's forces in an armored snowmobile before continuing in James' car. They rendezvous with Q, who takes them out of Austria.

After the breach, Drake threatens to kill Mayhew, should the operation fail. Mayhew contacts MI6, saying he will provide vital information if Bond comes to his rescue. At his Japanese estate, Mayhew is attacked by Drake's men, consisting of Japanese thugs. Bond fights his way through the estate and manages to obtain a file from Mayhew's safe. As they are prepared to make an escape from the estate, Mayhew is killed by a ninja. The file leads Bond to Mayhew's office at the Phoenix Building in Tokyo.

Bond is able to infiltrate the building while the guards are changing shifts and secures official NightFire documents. He is then attacked by Drake's men before Dominique provides a distraction, which allows Bond to escape via parachute off the roof of the building.

The NightFire documents lead Bond to a nuclear power plant being decommissioned by Phoenix International. Bond retrieves evidence of Drake's activities and escapes. However, he is then double crossed and captured by Kiko, Mayhew's former bodyguard, and turned over to Drake. On the top of the Phoenix building, Drake plans to kill Bond and Dominique, who has been discovered as a mole. Dominique is kicked off the rooftop and killed by Kiko. Bond escapes to the ground level before being saved by Australian Intelligence agent Alura McCall.

M sends Bond and Alura to Drake's private island, where Drake has set up a jamming signal. The pair infiltrate the island and eliminate Drake's defenses. M makes Bond aware of the UN, EU, and NATO forces arriving on the island to dismantle remaining enemy combatants. Bond makes his way to Drake's underground silo, fighting off Kiko before entering one of three space shuttles intending to capture the Space Defense Platform. Kiko incinerates in the blast pit when Bond's space shuttle launches. Bond reaches the U.S. Space Defense Platform, where Drake is. He successfully sends all eight missiles off course, saving millions of lives, and causes Drake's laser weapon to malfunction, leading to a huge explosion. Finally, Bond kills Drake. As the station goes up in flames, Bond blasts from an escape pod and goes back down to Earth, where M informs him that astronomers from around the globe are reporting "unexpected meteor showers" (which is actually the debris of the now-destroyed Space Defense Platform).