When Randy inadvertently mind-wipes himself and develops amnesia, Howard must fill in as the Ninja until Randy can get his memory back.
The episode picks up where the last picks up, with Howard in the ninja suit in place of Randy, fighting the Psycho-Bot, a learning robot who adapts to its opponent's combat moves. Since the robot had only fought Randy before, it does not recognize Howard's style, and is defeated by Howard. The excitement over his victory is overshadowed by the robot, revealed to have survived, now in hiding.
In the aftermath of the battle, The Sorcerer stanks the robot after detecting it developing emotions. Randy sees the NinjaNomicon, left behind by Howard, which pulls him in and restores his memories. He returns to find Howard fleeing from the Psycho-Bot, and takes back the suit. He strategizes a way to destroy the robot's memory chip. He defeats it.
When the students are returning to school, Howard concedes that he was not prepared to be a ninja. Principal Slimovitz makes the announcement that all classes are cancelled due to the destruction at the school, with the exception of history class. Howard and Randy's dam project is still due.
- This episode and "The Ninja Identity" make up the show's second special, the first being the "Dawn of the Driscoll" and "Night of the Living McFizzles".
- The title is play on the 2004 action spy film The Bourne Supremacy.
- The theme song was altered in this episode, Howard singing along and explaining how he has to replace Randy.
- This is the first time Howard has put on the Ninja Mask, and the second time he's dressed up as the Ninja, while the first time was in Monster Drill.
- The episode reveals that when a ninja has completed their training, they take the Ultimate Lesson to get their memory about being the Ninja erased and their experiences are published in the NinjaNomicon.
- The same conversation between Randy and Howard when Randy revealed he was the Ninja in "Last Stall on the Left" happens again in this episode, except Howard is the one telling Randy.
- Clips of the Nomicon from "Last Stall on the Left", "30 Seconds to Math", "Wave Slayers", "Weinerman Up", and "Gossip Boy" appear in this episode.
- This is the first time actual clips of the show have appeared in other episodes, although Nomicon lessons have been brought up before in "Raiders of the Lost Nomicon".
- This is the first episode where the Sorcerer stanks a robot.
- The reason how the robot got stanked is because it learned emotions with the memory chip Viceroy installed in it, learning humiliation, shame, and disgrace when Howard (while wearing the Ninja Suit) humiliates the robot.
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