The episode opens in a Kraang laboratory, with the Turtles secretly observing their discussions about swapping minds with human leaders in order to simulate another invasion. Raph prepares to attack, but Leo restrains him, wanting to hear more details about the plot. A Kraang is then ordered to bring a test subject into the equation and he does just that, bringing a human in and strapping him down to a metal table. When the human realizes that he is about to switch bodies with a pigeon, he begins to remark how he would prefer to have his brain probed into. The Turtles then seize the opportunity to attack, quickly taking out the majority of the Kraang. However, one Kraang triggers a device to tap into both the pigeon and the man's brains and swap them in a matter of seconds. Just after Raph releases the man, the latter starts to roam around the room like a pigeon - and Raph observes this in disgust.
Seeing as though their experiment is a success, the Kraang demand the Turtles to be destroyed and they begin firing at them. Meanwhile, a Kraang pushes Raph towards the side of the machine, but Raph quickly turns the tables and begins to attack the Kraang, much to Leonardo's aggravation. Raph pins the Kraang down, but just as Raph renews his attack with one of his sais, the weapon accidentally comes in contact with a part of the perilous machine and energy blasts start flying in various directions. This causes both Raph and the Kraang to be struck and knocked down. Leo quickly picks up Raph, while Mikey and Donnie rescue both the civilian and the pigeon. They then retreat. However, little do they know that Raph was not only harmed - but he had his mind swapped with the Kraang he was nearest to as well!
After dropping off the civilian the pigeon, the Turtles then begin to return home in the Shellraiser and Mikey attempts to reawaken Raph by slapping him in the face a number of times. When Donnie points out that is going to be futile, Mikey then decides he should try and 'tickle' Raph with some hand-spikes. This ultimately works and Raph starts laughing robotically, with an oddly stern expression on his face. Raph then puts his hands on Mikey's shoulders and asks what location he is in so that he can inform the Kraang. Mikey believes that all of this is a facade, but he soon figures out that it isn't at all, especially when Raph slams him against a wall four times. This makes every one come to the realization that a Kraang is now in Raph's body and is trying to eliminate them. A distracted Leo then accidentally collides with a row of parked cars, which allows time for the Kraang in Raph's body to escape onto the streets. Very uncertain about where to search for their actual brother, the Turtles retreat back to their hideout.
Meanwhile, the Kraang transport their comrade that has Raph inside of it to a facility where he can have his damages repaired. Raph soon wakes up and begins to realize that he is inside of a Kraang's body, but tries to stay calm. After being able to fool the other Kraang with his 'best' impersonation of them, Raph narrowly escapes and discovers that he is inside the Technodrome, which had landed on the ocean floor, much to Raph's utter disappointment.
Meanwhile, the Kraang (in Raph's body) walks along the streets and attempts to ask random people where he could find the Kraang, to which they respond by merely running away. The Kraang then glares at himself in a storefront window and remarks that he is in the body of a monster - after a woman refers to him as this. The Turtles then ambush their false brother in a back alley and bring him into a dumpster.
Down in the Lair, Casey watches an episode of Super Robo Mecha Force Five!, in which the team of protagonists are able to outwit yet another one of their enemies. Casey comments that the show is pretty cool, in spite of the fact that he dislikes dubbed anime due to lack of audio sync. Soon, April and Master Splinter are both seen exiting the Dojo, with Splinter telling April that her skills have been continuing to improve without pause. Splinter tells her to remain patient with herself and April confesses that she could practice all day. She sits down next to Casey, all sore from training, and Casey offers to give her a massage. Jokingly, April refuses, much due to the fact that Casey has greasy 'pizza fingers'. Then, Leo, Mikey and Donnie enter the lair with 'Raph', who has a grocery bag covering his entire face. After Leo tells both Casey and April about the awkward circumstance, Casey begins to laugh hysterically, while Splinter steps in and wants Leo to describe everything that has occurred.
Back in the Technodrome, Raph (in a Kraang body) continues to walk around, trying to locate the nearest exit. Another Kraang spots his 'comrade' facing away from him, so Raph, in a poor impression of Kraang speech, asks where to find the exit. The other Kraang is confused by his query and says that Kraang is busy. Once again, Raph pretends to act as they typically would and questions what he should be busy doing. The Kraang then walks him into a communication room, where two other Kraang are standing. A transmission from Kraang Prime then appears, stating that the Kraang in Dimension X are starting to assemble for the invasion of Earth. Raph spots a Kraang Communication Device similar to the one that Donnie has. Kraang Prime then directly addresses the Kraang responsible for Plan 10 for a progress report, which happens to be the Kraang Raph is in. Raph (in his impersonation of Kraang) states that the Plan 10 is 'Kraangtastic'. Satisfied Kraang Prime orders Plan 10 to be implemented. When all the other Kraang leave the room, Raph quickly uses the orb to try and find a way to communicate with Donnie.
Back at the Lair, Leo finishes his explanation to Splinter, and he, Donnie, Mikey, April, and Casey are all about to mobilize to retrieve Raph's mind, but Splinter halts them and reminds them that they should consider being patient instead, as the impatience that Raphael had is what landed him in the den of the enemy. April then asks what their secondary option would be and, before Splinter can fully reply, Donnie's Kraang Communication Orb starts to buzz in his lab. The gang then goes to investigate, and Donnie remarks that the device hasn't been active for months. He then boots up his laptop and the face of a Kraang droid, who is actually Raph, immediately appears on the screen. Raph then reiterates to them that he was trapped in a Kraang's body. Casey then starts to openly tease Raph by laughing, but stops when April nudges him. Believing that the Kraang could easily imitate Raph's speech patterns, Mikey asks Raph to tell them what the 'secret ninja password' is. Raph angrily replies to Mikey's ridiculous comment, which Mikey considers to be 'close enough'. Donnie then brings up Raph's coordinates, which reveals that he's located under the surface of the East River near its confluence with the Bronx River, not far from Manhattan. Then, Donnie says that they may have to do some swimming.
Back at the Technodrome, Raph (in a Kraang body) just finished contacting Donnie with the Kraang communication orb, and at the worst time possible, two Kraang walk in, and ask their 'comrade' about who he just contacted, as the communication orb was not to be used at that moment. Trying to fool the Kraang, Raph (doing his Kraang impression) insists he was talking to other Kraang. Another Kraang asks why 'Kraang' did not report for vitamin infusion. Raph bluffs that he forgot. The Kraang then state that they never should forget things.
Meanwhile, the Turtles, April, and Casey all begin their search for Raph in the Turtle Sub. Casey complains about the weaknesses that the vehicle has, only for Donnie to logically describe the Sub, including it's physical powering source. Leo then lowers the periscope, noticing that the Technodrome is straight ahead. Mikey happily states that they are now home free since they are practically at the destination. Unfortunately, he states this just when the Kraang's Water Creature shows up - and Donnie angrily yells at Mikey for what he said previously. The creature then roars at the Sub, but then cuddles it for a second and leaves, leaving April completely clueless. The creature comes back, offering the Sub some garbage to 'eat'. Disturbed by this, Casey, April, and Leo start to power up the Sub, just to escape the creature. This makes the Water Creature sad, and, thus, it then follows the Sub. Not long after, the team believes they have gotten past the danger, but Donnie then detects the beast on Sonar, and their Sub is ambushed once more. They attempt to distract the creature with torpedoes made out of bottles, but when this fails for the most part, Donnie boots up the engines since they now have gathered enough foot power. This causes the sea creature's tongue to get stuck in an engine. After pulling it out, the creature flees into the depths, as soon as the gang escape.
Back at the Technodrome, the two Kraang that caught Raph (in a Kraang body) earlier order him to be completely analyzed. Raph (in his Kraang impersonation) asks what would happens if he was to refuse, and then one of the Kraang pull out their laser guns, and aim it towards Raph, telling him that they will need to take the necessary actions to protect their kind from harm. They then try to destroy their false comrade, believing him to be defective. They manage to obliterate the robot body, which forces Raph (who has taken the form of the Kraang brain itself) to flee the scene and rely on only his tentacles. Raph manages to find his way into a small lab where a bunch of inactive robot suits are standing. Raph initially freaks out at the sight of them, but then comes up with an idea.
Meanwhile, the three other turtles, Casey, and April breach the Technodrome and enter, just when an alarm sounds and the Kraang close in on them from all directions. One Kraang then tells them that they have been captured and will exterminate them shortly, but Raph, who is now concealing himself in a different robot body, stops his 'comrade' and tells him that they should spare the Turtles so that they could swap minds with them. He then claims that this was one of Kraang Prime's demands. The Kraang reluctantly agree with him and walk away. Raph then accuses his brothers of having their presence revealed so easily, and Mikey and Casey then begin pressing Raph's inadequate face, insulting him humorously and commenting that he feels like chewing gum. Raph, after pushing them aside, vows to make everything right again and tells his brothers to follow the Kraang.
This ends up working and they encounter the Kraang, just when the villains are about to activate another one of their mind-swapping devices. Raph tells a nearby Kraang that the Turtles will become part of the experiment. When the Kraang refuses, Raph throws a Sai into the center of its head and a battle starts. Donnie immediately runs to the neuro-switcher to try and find a way to restore Raph to his normal body. Mikey deliberately interferes by pressing tons of random buttons, which forces Donnie to knock him out of the way...However, Mikey ends up partially activating the targeting matrix. Donnie then fully activates it, which, unfortunately, causes April and Casey to switch minds, as they were the nearest to the device. Casey then examines 'his' body, which causes a frustrated April to scold him. She then tells Donnie to switch them back right away, and Donnie ends up getting slightly confused about each of their identities...Meanwhile, the Kraang in Raphael's body (who the Turtles were forced to bring along with them) frees himself and personally goes after Raph. While fending off other Kraang, Raph claims that he has finally been able to understand the bodies' abilities. Just then, the false Raphael appears and aims a Kraang gun at the actual Raphael. The two then battle and The Kraang in Raph's body gains the advantage when the actual Raph realizes that his life would be ruined if he was to stab himself!! Donnie, noticing that the two 'Raphaels' are now within range of the matrix, presses the correct button and transforms both of them back to their original forms. Raph then defeats the Kraang that opposed him and joins his brothers. Casey and April's minds are also reverted as well, just before Donatello sabotages the device and he and every one else escapes safely.
Back at the lair, the gang is watching SRMFF on the TV while Raph is very pleased to be back to his normal self. He even expresses his pleasure by saying thanks to his brothers, much to their surprise. However, Raph then states his displeasure about not being able to destroy the neuro-switcher, but how he also witnessed the thousands of soldiers that the Kraang have ready for a second invasion. Leo then asks Master Splinter how they would be able to stop this. Splinter states that a solution might arise; in time. Donnie then reveals to his brothers that he has been working on a complex sketch of a ferocious weapon they could possibly use to stop an invasion, which Mikey responses to Donnie that he's a bigger genius than he is.
"Michelangelo: That's too big to be a probe, right?"
"Kraang: The Kraang neuro-switcher will switch test subject's mind with that what is known as a pigeon.
Man: I think I'll prefer the probing"
"Casey Jones: This show's cool, but where are the subtitles? I hate dubbed anime"
"Raphael in Kraangdroid body: I feel great! I mean, uh... Kraang is feeling much, um, Kraangier."
"Michelangelo: You feel like chewing gum!
Casey Jones: This is so wrong!"
"Michelangelo: Donnie, you're an even bigger genius than I am."
"Casey in April's body: Cool."
"April in Casey's body: Stop pinching your own butt, Casey!"
The episode's title is a reference to the 1959 sci-fi film, Plan 9 From Outer Space directed by Ed Wood.
This episode has a similar premise to the 80's TMNT episode The Old Switcheroo where Splinter and Shredder switch bodies, as well as the episode Raphael drives em wild where Raphael switches bodies with a cabbie named Oscar.
When Raph and the Kraang switch bodies they also switch voices too, but in the show they both sound the same to everyone in the show. This is so the viewer won't be confused.
In the scene where Raph escapes from the other Kraang he is making various noises that Jerome Lester Horwitz, better known as Curly Howard of the Three Stooges, made during his career as Curly.
For a brief moment we see Mikey wearing his white undies in the final scene.
Skelelord, the villain in SRMFF, is an obvious parody of Skeleton King from Super Robot Monkey Team Hyperforce Go! and Skeletor from He-Man.