C.I.A. Agent Sean Davidson (David Bradley) is sent on a new mission. It turns out that the situation is really grave one. Colonel Scott Mulgrew (Booth) an anti-American Army officer from Britain has sided with Sheik Maksood (Ron Smezarack) a Muslim militant who are planning to use a suitcase nuke to erase New York from the face of the earth. They also are training a secret Ninja Army in an old British fort. Mulgrew's army captures four commandos from a Delta Unit force run by the African government, and Mulgrew threatens to burn those commandos alive and nuke the Big Apple until he is paid 50 million dollars. The local Police chief also supports him. Sean and his sidekick Carl are parachuted near the fort.
While gathering information from a few local operatives they are pursued by the police. While escaping, they come across Doctor Sarah (Robin Stille) a peace corps nurse. However in a nearby jungle, the Ninja Army attack them. Sean and Carl fight with the ninjas using their guns, nun chucks, bows and arrows, however they are captured and Sarah, Carl and Sean are imprisoned in the fort and tortured by Mulgrew and a Ninja master. Joe Armstrong (Michael Dudikoff), a special forces commando is lured out of retirement and he is sent to help Carl and Sean. Meanwhile Mulgrew tries to rape Sarah and it turns out that Mulgrew killed Sarah's father.
Now, with the help of some Local rebels known as Sulphur springs, Joe learns Mulgrew's location and equipping himself with Ninjutsu equipment he enters the fort stealthily, killing a few ninjas. Mulgrew decides to execute Sarah, Sean, Carl and the delta force commandos. Joe then attacks and rescues all the commandos and Sean and Carl and Sarah. Meanwhile the local rebels also attack the fort by massacring the opposing police forces. Mulgrew and Maksood's whole army is wiped out and the nuke is defused. Maksood tries to run away in his helicopter. Carl fires a missile, destroying the helicopter and killing Maksood. The ninja master is killed by Joe and Mulgrew is killed by Sean. Joe shakes hands with the leader of the rebels. He then bids goodbye to Sarah and Sean. The film ends with Joe walking away through the heaps of dead bodies of the Ninjas and the debris of the destroyed fort.