Episode starts probably a couple weeks after the Finale as the Turtles are on the surface partying, and reoccurring events that happened to show their awesomeness to each other. Donnie then tells the others they should go see April. April when they meet at her apartment says that her dad is having terrible nightmares about the Kraang abduction and has been keeping April from leaving at night in fear. The turtles swear that April and everyone will be safe being the Kraang & Shredder are gone, but it's revealed that Shredder has contacted the Kraang about receiving a shipment that will be arriving shortly.
(The only differences in the Title that I recall was the Shredder scene with Fishface & Dogpound now has a scrolling effect of numerous villains that include SpiderBytes, Snakeweed, The Rat King, Newtralizer, Karai, Kraang, Shredder and some others. Also in the Donatello part of theme, you now see Metalhead walking on screen while Donnie is doing his regular bit.)
Leo, Mikey, & Raph are then playing Ninja Dodgeball with the Kraang Communication Orb while Donnie is in his lab beginning the first steps of building Timothy's suit (So it does appear that Donnie will make the suit for him) After a harsh lecture from Splinter saying the Turtles have become lazy and cocky since the Kraang's defeat, the Kraang Orb starts going off signaling that the Kraang are back. Donnie learns that the Kraang are using a Stealth Ship to carry whatever they have for shipment and has designed a tracker (The Game Boy looking contraption) to find it. He tells April to take to the surface though she claims she would have no clue how to use it, then they ask if her dad would which leads to April and her on the roof while the Turtles attempt to break into the ship. During the fight in the ship with the blue Gorilla Kraang they discover that the shipment is hundreds of canisters of mutagen and after a critical error opening a cargo hatch in the ship, all the mutagen canisters fall out of the ship and into the city.
One canister looks like it's about to hit April, but her dad shields her from it causing him to mutate after Kirby falls from the roof, bats fly all around him and trigger him to mutate into a bat. After the Turtles escape the ship they see the mutant bat staring at April and begin to attack, but April tells them to stop, during the distraction, Kirby freaks and grabs April and flies off.
Back in the sewer, the Turtles from come up with a plan and after Mikey wonders what silly sucker would be used as bait, the Turtles put Mikey in a ridiculous fly looking costume. (Mikey calls himself "TurFlytle") The Turtles go out to find Kirby while April is trapped on a ledge on a tall building. Raph and Leo use Mikey to attract Kirby (Mikey does call him "Wingnut", which Donnie threatens Mikey to not give April's dad a monster name) After Donnie is knocked out of the sky, he finds April and gets her off the ledge while the others are barely able to get Kirby to the warehouse and trap him in a cage just as April arrives.
April asks the Turtles what they can do for her dad and she says that everything is her fault for lying to her dad. But Mikey goes to her and says that it wasn't her, that it was their fault for spilling the mutagen over the city. April though then is taken aback and confronts the Turtles for the mutagen spill and after a bitter exchange, Kirby breaks out of the cage he is trapped in and goes back on the attack, after Donnie strikes Kirby to protect April, Kirby flies off and escapes and April is now furious at the Turtles for her dad now gone. Donnie begins to say something and reach out to her, but April shuts him up and tells him to not touch her and that she never wants to see the Turtles again and runs off. Donnie begins to run after her, but Raph stops him and says it won't do any good and to just let her go, crushing Donnie.
After learning of the failure of the Kraang, Shredder decides to cut ties with the Kraang and decides to find his own army to assist in his vendetta.
The episode ends with the Turtles back in the lair with Splinter telling them to not dwell on the past, but rather on how to fix the future, and the episode ends with a squirrel running up to a broken mutagen canister and licking and his eyes get all glowy in "Dramatic Chipmunk" style, ending the episode.
