Dark Island Scarlett is having doubts about herself, not concentrating during a training exercise and worried about how Ninja Force treats her. Hawk reminds her of a mission from when she first started as a Joe, leading to a flashback story.
Hawk briefs Rock 'n' Roll and Breaker on a mission involving the fortress named Safe House on a Caribbean Island, run by Madame Umbra. Umbra is suspected of routing funds to terrorists, so their mission is to shut down the operation. The plan is for Scarlett to be disguised as a spy, and for Breaker and Rock 'n' Roll to deliver Scarlett to Umbra in trade for an American scientist.
The trio lands on the island, and is escorted to Umbra. Umbra sends Breaker and Rock 'n' Roll to their quarters to await their merchandise. Rock 'n' Roll notices the door is locked, and Breaker is able to unlock the door. Breaker attacks a technician and steals his uniform, and gets to the main room of the base.
Scarlett attempts an escape, and learns that the American scientist is actually a Russian spy sent to do the same thing the Joes are trying to attempt. The two spies are both recaptured, and Umbra kills the Russian spy. Once Umbra realizes who Scarlett is, she challenges her to a fight to the death.
The guards realize that Breaker is no longer in the room, and Rock 'N' Roll escapes to the main room also. Breaker is retrieving information from the computers tying Umbra to Cobra and other terrorist organizations when the guards attack him.
Scarlett, Rock 'N' Roll and Breaker all regroup, and Breaker stays behind to get a distress signal to the submarine that dropped them off. Rock 'n' Roll and Scarlett escape the fortress into the surrounding jungle, but Scarlett stumbles into quicksand. Rock 'n' Roll saves Scarlett from the quicksand using a tree and his brute strength.
Scarlett and Rock 'N' Roll are cornered by Umbra and her men, but Breaker shows up and detonates Umbra's fortress, Safe House. At that point the sub surfaces with reinforcements. Not wanting to be taken alive, Umbra uses Scarlett's gun to kill herself. The submarine takes the Joes to their next assignment.
Back to the present, Hawk tells Scarlett she's done great things since that first mission. Scarlett agrees to try the training exercise again and passes easily.