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 starts with Howard wearing the mask. Howard and Psycho Bot fight, but the robot fails to defeat Howard as his tactics are different from Randy's. Howard humiliates the robot until it runs away crying as everyone cheers except Randy and Theresa Fowler. Howard is happy over his Victory, but not long after, the robot is seen hidden. the Sorcerer, upset about McFist and Viceroy's failure, senses the robot's artificial emotions and stanks it. Randy notices that Howard left the NinjaNomicon behind and as Randy opens the book he gets sucked in. There, the Nomicon reminds Randy of who he is and once Randy remembers and exits the book, he finds a distressed Howard running away from a stanked robot. Randy gets the mask from Howard near the Norrisville Dam after the robot threw them down. After fighting the regenerating robot for a bit, Randy realizes in order to de-stank it and shut it down for good he must destroy his learning and memory chip. Once Randy does that he successfully defeated the robot. When Randy and Howard get back to school, Howard finally admits maybe Randy was right about the entire there's more than being a ninja and Howard was wrong. Principal Slimovitz announces that the school is completely destroyed and that classes are cancelled. Everyone rejoices. Before Randy and Howard get to rejoice, they are informed the History class is intact and fine and they can still do their project. Randy and Howard are completely bummed at this news and the episode ends.
- 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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