One month previously the World Liberation Army had launched a surprise attack on Venice, Italy, and a week after that an attack on several Asian networks. Phoenix tries to convince Roux that the attack on Venice was a cover-up for something greater, but Roux does not believe him. The cutscene ends, and the game begins as a flashback, with Phoenix and Bull infiltrating Venice as part of a Gilman Security Special Forces Unit.
After moving through the buildings of Venice, shooting WLA soldiers, Phoenix and Bull hijack an enemy boat. They escape through the Grand Canal, gunning down enemy boats and helicopters with a mounted turret. After the mission ends, another cutscene begins with Phoenix and Roux continuing their conversation.
Phoenix further tries to convince Roux that something big is about to happen, even insinuating that Gilman Security is involved, but before Roux can respond the room they are in is attacked. Phoenix blacks out. Roux calls Tukura to rescue Phoenix.
Phoenix wakes up a month later in Rinnoji Temple, Japan. The temple has been converted into a makeshift hospital, and is under the control of the Raiders. It is the first day of the International Summit on Cyber-Security, and Tokyo has become a battleground.
Miku Kubo leads Phoenix out of the building, where he meets up with Tukura and Andrews and heads towards downtown Tokyo.
Immediately after reaching downtown, the truck in which the group is traveling in is ambushed by the Raiders. Phoenix tries to hold them off using the 50 Caliber mounted on top of the vehicle, but eventually the truck is flipped. Tukura drags Phoenix away from the wreck just before it explodes, likely killing Andrews.
They venture into the city on foot, gunning down every enemy in their way. In addition to Raiders, they also combat Gilman Security tricopters, drones that have been instructed to fire upon everyone. Eventually, they reach a safehouse. Once in the safehouse, Phoenix grabs a sniper rifle, climbs to the roof, and begins defending the building from the swarming Raiders.
After a couple minutes of sniping, an Apache helicopter appears and launches a rocket at the building. The explosion blows up part of the roof, causing Phoenix to fall off. On the ground, Phoenix reenters the building and continues holding it off against the Raiders.
Soon he is joined by Roux and Hawk, and they bring the battle outside to the courtyard.