The episode opens with an episode of Crognard the Barbarian, but it is interrupted due to the Channel 6 Breaking news. The anchorman says that New York City is off limits under military order. The Turtles suspected of this while watching TV. They decided to break through the New York City barriers using Donnie's plan for a new vehicle. They converted the old van with new gear, weapons, and a new paint job, turning it into the Party Wagon. With the vehicle all set up, they ready to go to New York City.
As the gang prepare to leave the farm, they hook up the Turtle Racer to the van. Donnie bids farewell to Dr. Cluckingsworth while April says goodbye to the farmhouse. They soon drove off and headed back to New York City. Upon arriving New York, Leo says that the first that they must find Splinter, then Karai, an then take back the city. Their plan was to park outside the gate and sneak in, but that proves impossible when soldiers have every entrance into NYC quarantined. April then notices that the troops have Kraang mind control devices on their necks, so Casey simply floors it and the Party Wagon is able to smash through the gates and into the city.
Inside the city, everyone was gone. Mikey wonders if the Kraang mutated the entire population. April says she is picking up thoughts from only a few hundred people, meaning there are millions missing. They soon run into Kraang soldiers, so the Turtles get to test out the Party Wagon’s soda cannons and stink bombs, both of which prove effective as they make their escape.
Using the Shellraiser's old subway access hatch, they enter the subway, The group does some effective ninja-ing, evading Kraang robots. Donnie ask April if she can use her powers to find Splinter. But April said that since Splinter's spirit has detached from his body, she’s not sure what has happen to him. Mikey decides to start searching for him at the lair.
At the lair, the turtles search for Splinter, but there is no sign of him, but the Kraang does have a robot security system that ends up using lasers to exterminate a ordinary rat. Mikey freaks out and wants to move back in, but the others thinks that’s not an option. Suddenly, April gets a faint read on Splinter, who seems to nearby, but he’s different somehow.
After the gang follow April, they find Splinter, only to discover that instead of acting like an experienced ninja, he acts like a savage rat, biting and attacking anything in his path. As they try to calm Splinter down (including keeping him from chewing Casey’s face off), and talk some sense to him, a Mouser calls in for backup, and Foot soldiers appears. Despite their best efforts, Splinter gets captured by Foot soldiers and is brought to the Shredder.
At Shredder’s Lair, Tiger Claw is concerned that the Kraang desire to conquer Earth and eventually betray the Foot. Shredder is aware of the situation, and assures that soon they will eliminate the Kraang and claim control of the city. The Foot soldiers return with Splinter, which surprises both Shredder and Tiger Claw, who believed him to be dead. Seeing Splinter, who clearly lost his mind, Tiger Claw asks if he should put the rat out of his misery, but Shredder disagrees and has him taken to Baxter Stockman instead.
In his lab, Baxter was working on his own retro-mutagen when the Foot soldiers bought Splinter to him. Shredder orders Baxter to restore Hamato Yoshi’s mind, so that he’ll understand what is happening when Shredder finishes him.
The turtles find an access tunnel that leads to Stockman's lab, only to come under attack by a miniature Shredder clone. After a quick battle, the gang find Splinter, still behaving like a rat. Casey then suggests that April should try to reach Splinter's mind like she did with the Turtles in their dreams. Donnie suggest that may work. But before they could do it, Baxter spotted them and quickly unleashes all three of his Shredder mutants. As the turtles battles the mutants, Mikey accidentally sets off an alarm, alerting both Shredder and Tiger Claw.
While the turtles fight, April tries reaching out to Splinter with her telepathy. He begins to get flashes of his memories back, but he mistakes Casey for Shredder and attacks him. Splinter then ends up charging at and cornering April, but from that range, her powers work even more effectively, and soon Splinter is once again himself. He quickly recuses the turtles and manages to defeat the Shredder mutants. The turtles rejoice that Splinter is back, but their reunion is interrupted when Shredder and Tiger Claw arrive. Realizing that now this isn’t the time for a fight, Mikey uses a ninja smoke bomb to covered their escape.
As they escape with the Party Wagon, Tiger Claw appears, holding onto the roof. With the use of Sir Siz-L-Lot, a flamethrower concealed inside a deer head that used to hang on the farmhouse wall, Tiger Claw is knocked lose as they drive out of the subway and into the city.
As they drove, Mikey wonders where they will live. Splinter says homes are transitory, but Leo points out they still need a place to hang their masks. Mikey then has an idea. They decide to use Antonio’s Pizza-Rama as their hideout for the time being. But April is still worried about her dad, and her power are giving her a weird reading on him and the missing people. It’s like they are right around them. We soon briefly see what April sees: a bunch of Kraangatized people mind-controlled by the Kraang including her Father.
"Wizardess: Crognard, megalord zarrik's soldiers guard the entrance to the fortress of the ragnaroid.
Megalord sarrik's: You will never get through the gates of eternal stagnation, Crognard. Hahahaha...
Spooch: Eh, spooch spooch! It's impossible, Crognard! What are we going to Spooch?
Crognard: Crognard must think. Spooch will storm the walls and distract the zarrik army
"Carlos Chang: Ever since the invasion that is known as the invasion of new york, humans want to know what is going on. Everything is...Fine. No human is allowed in or out of the city until kraan--uh, the military allows it. This is carlos kraang o'briengambe.
Mikey: Hmm, did the news guy seem a little kraang-y to you?
Raph: A little? What, are you on the pepperoni?
April: The kraang may have the rest of the world fooled, but not us. What's the plan, leo?
Leo: Step one is, storm the castle walls. Donnie?
Donnie: It's not as heavily armored as the shellraiser, but it's more maneuverable, has more weapons, and gets better gas mileage.
Casey: Then let's stop jabbering and build this sucka!."
"Donnie: Ehem. The new and improved... Party wagon!
Raph: It's so awesome!
Leo: All right, team. Let's do this!"
Mikey: Come on, ice cream kitty. We're going home.
Donnie: Dr. Cluckingsworth.
Dr. Cluckingsworth: Hmmm??
Raph: You both sicken me.
April: Good-bye, old farmhouse.
Mikey: Hello, new york city!"
"Leo: All right, team. First, we track down master splinter. Then we hunt for Karai and free the city.
Raph: So what's the plan, fearless leader? Ninja-y or all-out attack?
Leo: Ninja-y. We park at the gate and sneak in. Then we split up and search for master Splinter.
April: And my father.
Donnie: Okay... Not good.
Mikey: Oh, man! They got us, dudes! The jig is up, homeslice!
Earth Protection Force Soldier: Citizen! This is epf quarantine sector 7-b. Roll down your window. Authorized personnel only. No one goes in or out of new york city.
Casey: Whatever you say, army dude.
April: You see that? It's a kraang mind control device. I bet they all have them.
Mikey: They're all controlled? Like.. Invasion of the brain suckers?
Leo, Donnie, Raph, Mikey: Whoa!
April: Aaaa!!! What are you doing, Casey?
Earth Protection Force Soldier: Stop!"
"Raph: What were you thinking, man? You got any brains behind that hockey mask?
Casey: I had no choice, raph. They were powering up their blasters.
Donnie: Um, guys? Where are all the people?
Mikey: You--you think the kraang mutated everyone?
Leo: No way, not possible.
April: It's completely possible. I only sense a few hundred people left in the entire city. They're...Gone. Millions of people just...Gone!
Mikey: One good thing: We haven't run into any kraa....
Kraang: (See April And Casey Jones)
Mikey: Oh, no! Why did I have to open my big mouth?
Kraang: It is the humans known as casey jones and april o'neil. Kraang! Eliminate for kraang!
Leo: Man the defenses.
Mikey: Readying soda cannons.
Donnie: Loading breath mints.
Kraang: Aah!! It stings! It stings!
Raph: Bomb-a-pult locked and loaded. Launch!
Kraang: Uh-oh. Argh.... You can smell it. That which is known as stinks. Pee-yew!
Casey: Time to go.
Donnie: Take a left. There's a secret entrance to the subway right here."
"Mikey: You think we'll be safe down here, dudes?
Leo: Shh, full ninja mode.
Raph: You hear that?
Leo: Phew, that was close.
Donnie: April, you think you can use your powers to track splinter? You did it before.
April: I can try, but... You said his mind is no longer one with his body, right? Which means he could be crazy.. Or unconscious.., or. Or who knows what?
Donnie: Yeah. We still need to find him.
Mikey: Ooh, what about the lair?"
"Leo: All right. Mikey, you stay here.
Mikey: But I want to...
Kraang Security System: (Shoot Everything At Donnie And Raph)
Donnie: Ah! Whoa!
Kraang Security System: (Looking A Rat And Shoot)
Donnie And Raph: Ah!!"
"Leo: No sign of Splinter.
Raph: The kraang have some kind of freaking security system to make sure we don't come back.
Mickey: Why not just go take it down and move back in? I miss our home. I miss my comic books, my vhs tapes, my action kick unicorn man, my collection of human underwear.
Donnie: It's not that simple, mikey. We can't just move back.
April: Guys, I-I think... I think I sense splinter close by. It's faint, and he seems...Different. Come on, hurry."
Splinter: (Hissing to them)
Casey: Whoa!!! Ah!! Ah, get him off of me! Get him off of me!
Donnie: It's okay, Sensei. It's us! We're your sons! Try to remember.
Mickey: Ugh, too strong!
Leo: Sensei, it's us. It's us. Calm Down.
Donnie: Oh, no! Foot!
Leo: Get ready, team. Don't let them harm splinter.
Raph: Oh, no. Splinter.
April: There are too many!
Donnie: After him!
"Tiger claw: Master shredder... Your enemies are defeated. Do we wait for the lowly kraang to mutate the entire earth? Destroy all of humanity?
Shredder: Watch your tone with me, tiger claw. I am well aware of the kraang's plans. When the time is right, we will destroy
those putrid aliens, and the city will belong to me. Now...Keep searching for karai.
Tiger claw: What! It cannot be.
Shredder: Hamato yoshi lives? He survived, but not intact. He has clearly lost his mind, become the rat I always knew he was.
Tiger claw: Shall I put him out of his misery, master?
Shredder: No. Take him to baxter stockman."
"Baxter Stockman: Bzz. A little more arthropod dna, and thizz might create a pozzible retro-mutagen.
Baxter Stockman: Ah!
Shredder: I want you to restore hamato yoshi's mind.
Splinter: Grrr... Aaaa...!!
Shredder: I want him fully aware of who and where he is.. Before I finish him off.
Baxter Stockman: Yezz, mazzter..."
"Donnie: I'll have this baby open in no time. Like a turtle do.
Raph: Pat yourself on the back later. Let's move.
Mickey: It's shred-head.
Raph: What the heck is that supposed to be? Mini-shredder?
Mickey: Haha, it's kind of cute, like a shrimp.
Casey: What the heck? Ah, Ugh!
Raph: And stay out, you little freak!"
"Baxter Stockman: You want this cheese, don't you?
Splinter: (Smell the cheese)
Baxter Stocman: You want the nice swizz cheese, yeah? Hmm, come on. Take the cheese. Come on. Hahahaha....
Raph: I'm gonna squash that bug.
Leo: Sensei. Sensei!
April: It's okay. It's okay. There's got to be a way to reach him.
Casey: Red, remember the time you reached the through guys their dreams? What if you could, like, do the same thing for splinter? You know, mind-meld and stuff?
Donnie: Hmm, based on my research on telepathy, it might be possible. But there is only one way to find...
Baxter Stockman: What izz this? Bzz, turtles? Here? You were all destroyed!
Raph: How's this for destroyed?
Leo: Look out! April, try and wake splinter up.
Raph: Oh, no, you don't.
Mickey: Whoa! Aaaa!! Hold still, buzzkill!
Baxter Stockman: Ugh!!.., No!! Ugh. Ha. Let's even the odds. Hahaha...
Donnie: Sweet mother of mutations.
Baxter Stocman: Do you like my Shredder mutantzz? They make excellent watchdogs. Bzz."
"Leo: These guys are full-on armored. Ugh! Oh, no.
Raph: Ugh, Ah, Ooh! This guy's like fighting a four-armed dump truck.
Donnie: Hold still, you little dendrobranchiata. Ah!
Mickey: Wow! Whoo-Whoo"
Casey: Splinter? Wake up, Splinter.
April: You are not a rat. You are Hamato Yoshi.
Splinter: Ugh! Ah!
Casey: Not again!
Splinter: Aaaaa!! Ugh!
Mickey: Aw Yeah! Booya...Kasha. Kekeke... Huh?
Shredder: The rat has escaped!
April: Come on, master Splinter. Come on!
Splinter: (Awake And Hissing)
Casey: I got this, red.
April: Master Splinter! Look.
Splinter: (Looks All His Memories)
April: Master Splinter?
Raph: Yah! Ugh!
Donnie: Not the face!
Splinter: Yah! Hiyah!
Splinter: My sons
Mickey: You're back.
Donnie: I-I can't believe it.
Splinter: How I have missed you, my sons... And the rest of my family.
Casey: Just please don't try and eat my face anymore.
Shredder: So the turtles live. And the rat thinks like a man again. Now you will know when my blade is at your throat.
Leo: Wait, sensei.
Splinter: Yes, now is not the time to fight."
"April: Piew. Ah!
Tiger Claw: There is no escape! Groa!
Mickey: Hey, tiger claw.. Meet sir siz-l-lot!
Tiger Claw: Ah!!
Mickey: Haha! Party wagon in full effect, boy!
Donnie: We made it.
Raph: Yeah, by the skin of our shells.
Mickey: So where to now? We have no home to go back to.
Splinter: Homes are transitory. What matters is that we are together.
Leo: But we still need a place to hang our masks, sensei. Where are we gonna live?
Donnie: Well, there's the old power plant, or maybe an abandoned subway tunnel.
Mickey: Wait, I have the greatest idea ever!
Raph: Do we really want to hear this?
Mickey: It's secret, fortified, and no one would ever think to look for us there."
"Mickey: Perfect, right?
Raph: I wouldn't exactly say perfect.
Splinter: It will serve, for now.
Casey: Next up, take the city back.
April: And find my dad. He's out there... Somewhere. It's like he's right here. Right next door."
With this episode, the opening sequence gets its fourth update—the largest to date. It was last updated in Within the Woods.
Old: Raphael launches from the Shellraiser in the Stealth Bike. The Shellraiser abruptly skids to a halt, showing Leonardo and Raph inside, with Leo getting a blue portrait scene sprawled with "LEO". Leo is then shown attacking and taking down the training dummy in the lair. Next, Donatello is in his lab in the lair, performing maintenance on Shellraiser, with Metalhead and Timothy (as Mutagen Man) in the background. Donnie gets a purple portrait scene sprawled with "DONNIE". Michelangelo speeds by on his skateboard, stealing Donnie's last piece of pizza. Next, Raph is shown playing the pinball machine in the lair with Spike standing on his left shoulder. The game penalizes Raph for tilting the machine and he gets angry. Raph gets a red portrait scene sprawled with "RAPH". Next, Mikey is skating out of the lair's entrance. He gets an orange portrait scene sprawled with "MIKEY". He takes one bite of the pizza he stole form Donnie, then drops the rest of the slice on the floor of the tunnel. He skates into a round sewer tunnel, doing half-pipes along its floor and walls. Next, the camera moves through the lair, passing April O'Neil as she reads a book sitting on the tire swing. The camera ends with Splinter, who bangs the floor with the bottom of his walking stick.
New: Casey Jones is driving the Party Wagon with April in the passenger seat. It drives down an extremely steep slope onto a country road. Next, Leo is shown dressed in his Vision Quest gear, running through a forest of aspen trees. He stops, turns around and strings a yumi and arrow. Leo gets a blue portrait scene sprawled with "LEO". He is then shown chopping an aspen tree clean through with his katana. Next, Donnie is shown in his Vision Quest gear, standing on the gondola of the Turtle Blimp. Donnie gets a purple portrait scene sprawled with "DONNIE". The blimp moves further away, taking Donnie out of view. But Raph, dressed in his Vision Quest gear, jumps from the top of the blimp toward the camera, and blasts fire with his left hand. Raph gets a red portrait scene sprawled with "RAPH". Next, Mikey, dressed in his Vision Quest gear, is shown swinging horizontally around the trunk of an aspen tree. Mikey gets an orange portrait scene sprawled with "MIKEY". After swinging around the tree trunk a few more times, Mikey leaps to the sides of other tree trunks, jumping from trunk to trunk as he maneuvers through the forest. Next, Splinter and April are shown training in the dojo, April exactly mimicking Splinter's poses.
Old: The four turtles fire their grappling hooks into a wall, then slide down the zip line between buildings.
New: The Party Wagon and Bebop and Rocksteady's van are both driving down the same city street. Leatherhead is standing on the roof of the Party Wagon. B&R's van side-rams the Party Wagon, and Leatherhead leaps from the Party Wagon onto B&R's van just as the Party Wagon side-rams it. The two vans catch up to Mondo Gecko emerging in the foreground, riding his skateboard in the same direction, but B&R's van quickly overtakes Mondo and speeds past him.
The New Sequence runs for the rest of the season, is temporarily replaced in Season 4 by completely different space opening sequence, returns in City at War with new updates.
Much like other episodes, the events in the cartoon the turtles were watching, in this case Crognard The Barbarian, foreshadow the events of the actual episode.
The villain that appears in the Crognard cartoon is based on Man-E-Faces, one of the many characters from The He-man series.
The synthesizer-laden soundtrack of the episode, especially when the turtles were approaching the city, was a reference to the 1980s cult classic Escape From New York.
Incidentally that movie starred Kurt Russell, whose portrayal of Jack Burton in Big Trouble in Little China was the inspiration for Casey Jones.
The episode is the debut of the Party Wagon, a familiar vehicle that appeared throughout the franchise
Raphael painted a green woman with a red mask with the name "Venus" next to her on the left side of the Party Wagon, possibly a reference to Mei Pieh Chi from live action The Next Mutation series by Saban.
On the stink bomb it's read "foot stinks", the same words on the 1980's party wagon.
The brand of breath mints Donnie puts in the soda cannons are "Chillos" a parody of the real life brand Mentos.
Although the original Shredder Elite from the Mirage comics were just mutant clones of Shredder, each of these new Shredder Elite members were created from a different crustacean: Mini Shredder is a shrimp, Claw Shredder a lobster and Shiva Shredder a crab. Additionally, there were crabs on Stockman's desk, indicating the Shredder Mutants were recent experiments.