Tanzy has been fixing up the kitchen when after watching dishes, she spots some muddy footprints on the floor. She yells at Spencer, who says that he and the other ninjas have been downloading movies for the past 72 hours. Rogi comlains that they needed to get a internet connection. Tanzy suggests that there might be an intruder, but Spencer claims that there are none. A scientist suddenly appears behind Spencer, shocking him.
The scientist introduces him as Dr. Brains. Dr. Brains is a scientist that has been living in the ninjas' basement for quite some time. He has been waiting for the right moment to introduce himself, but his toilet backed up, forcing him to use the ninjas' toilet. Spencer directs Dr. Brains to the bathroom which was just down the hall, in which he goes in and makes a huge fart. Andre suddenly realizes that they have a basement.
The ninjas explore Dr. Brains's lab, where Spencer complains that Dr. Brains owes them rent, while Bartleby suggests that Dr. Brains could be a valuable addition to their team. Spencer looks around for anything valuable, when he suddenly opens a safe,hurting his balls, but then Spencer, Rogi and Andre looked into the safe realising that it is containing many chickens. Spencer, Andre and Rogi fight for one of the chickens when it suddenly explodes. Dr. Brains explains that he genetically bred the chickens to explode, saying that "it seemed like a good idea at the time." Dr. Brains also shows the ninjas a retractable colon scratcher. However, Spencer has enough of Dr. Brains's wierdness and demands him to move out. The alarm sounds off that the zombies have broken into the yard. Spencer thinks this is impossible, since the zombies can't get over the fence, but according to a monitor, they did.
The ninjas look outside to see that the Zombie Circ Disarray has invaded their house. An opera singing zombie lets out an annoying sound. Spencer complains that they have to stop that pretencious new age music. Andre complains that it was like having live lobsters shoved into his earholes. Bartleby warns that if they don't stop them, the Circ Disarray will take over the entire earth. The ninjas jump into action to attack. Rogi was grabbed by a giant blue with tiny black spotted zombie lizard's tail and slammed onto the house. Andre was doing a good job until he was flattened by a giant ball twice. Tanzy and Chris get tangled by cloth which was from a giant fire zombie. Spencer claims that Tanzy and Chris should've seen it coming a mile away, only to be caught by a magician zombie's purple cloth.
All hope seemed to be lost when the opera zombie sings again, but Dr. Brains's tank comes in at the nick of time and runs over the opera zombie. Dr. Brains tells the ninjas that he built the tank in his garage. Dr. Brains then uses his Chicken Gun to kill all the invading Circus Zombies, he frees Chris and Bartleby, Tanzy and Spencer from the cloth and reinflates Andre as well as freeing Rogi from the zombie lizards tail . After the battle, Dr. Brains goes back to the house to pack his belongings, but Spencer stops him. Spencer apologizes for acting the way he did and realizes that science is useful, allowing Dr. Brains to stay. Dr. Brains claims that they won't know that he's there. Later that day, the ninjas were watching TV, not minding that Dr. Brains has farted very loudly again.