Some TMNT stuff really isn't for little kids.
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Professor Honeycutt, also known as Chet Allen, also known as the Fugitoid, has an existential moment atop a cliff on Burnow Island. In a moment of hopelessness, Honeycutt steps into nothingness and shatters to pieces on the jagged rocks jutting out of the ocean. A short while later however, General Krang's scientists have retrieved and reassembled Honeycutt's robotic body, and continue to download his scientific knowledge in order to complete work on the Technodrome, Krang's tool to terraform the Earth.
Meanwhile, Krang ensures that his staff has taken necessary measures to avoid loss of power as a result of an approaching hurricane. However, Baxter Stockman has snuck outside and tampered with the power system.
On pre-historic earth, a number of Utrom scientists arrive via a transdimensional portal. Two of the scientists discuss political trouble back home, the D'Hoonib people rebelling against Prime Minister Quanin, while they take samples from a triceratops.
Many years later, a much younger General Krang is celebrating the defeat of the D'hoonibs and the destruction of the Praxoid Alliance with his men, among them Zog, a Triceratons (a race of mutant triceratopses created by Utrom scientists). His father, Emperor Quanin walks in and asks what the commostion is for; Krang informs him that they have defeated the alliance.
In the Molta VI Asteroid Field in deep space, a crew of Utroms attempts to find ooze to harvest. Just as another asteroid fails to yield any ooze, the Utroms are fired upon by a rebel ship, manned by Neutrinos and Triceratons.
Months later, a meeting is being held on Utrominon in the High Council Chambers. Emperor Quanin reports that the rebellion continues to grow stronger and they must increase their military efforts to maintain their control over the edges of their empire. Quanin appoints Krang to the Praxoid Viceroyalty to oversee their mining and military operations. Councilor Lorqa interjects to ask why they continue to press outwards, colonizing new planets and enslaving new races. Quanin retorts that he had to interceed to avoid a power vacuum caused by the Praxoid Alliance's defeat. Lorqa accuses Quanin of bringing ruin upon his own people, throwing all their resources away on the expansion of his empire.
On Burnow Island, present day, the power goes out during the storm thanks to Baxter Stockman's sabotage of the power system. Stockman leaves his room and finds the Fugitoid being held in an examination room. Stockman frees the Fugitoid and tells him he wants to use the cover of the storm to thwart Krang's efforts. Fugitoid, planning on destroying his body so Krang can no longer use his knowledge, agrees to help Stockman.
In New Quanin City, the Seat of the Praxoid Viceroyalty, Krang is briefed on the current state of the fight against the rebellion by Commander Zog. Zog tells him that as a result of him ordering public executions for the miners who led the uprising, more people have joined the rebellion. Krang tells him that they can start killing the children of the rebels. Zog tells Krang that its not his problem anymore, just as a blast shatters the windows. Outside, a fleet of ships swoops down upon the city. Krang orders Zog to arm the Triceraton forces; Zog tells Krang to look outside, where the Triceratons themselves are the ones attacking the Utroms. Krang looks back at Zog who is pointing a gun at him. Zog tells Krang that his pride has blinded him to the futility of his father's efforts to maintain his empire. Krang knocks the gun out of Zog's hand and the two fight. Krang tells Zog that his people should be grateful for the elevation of their species, the bestowal of purpose. Zog manages to defeat Krang, but leaves him alive because he believes that Krang will realize his people are doomed if they continue on their current path.
In Northampton, Massachusetts, present day, Donatello searches furiously for something. Michelangelo asks what he's looking for; Donnie tells him that after Fugitoid was kidnapped by Krang, April broke into his StockGen locker and found his journal. Donnie, finally finding it, looks through and finds designs for the Technodrome.
On Burnow Island, Stockman and Fugitoid walk unnoticed through the building. Fugitoid tells Stockman that if they wish to destroy the Technodrome they have to go the other direction. Stockman tells Fugitoid that he's insane if he thinks they're going to destroy the most powerful weapon ever invented. Stockman shows Fugitoid where they were headed, the room storing the other Utroms in stasis, suspended in huge vials of ooze. Stockman tells Fugitoid that his plan is to hit Krang where it hurts the most, to destroy his purpose. Stockman opens the vials of ooze so that they start to drain and kill the Utroms. Fugitoid, deciding that he cannot simply destroy himself to keep his knowledge from Krang, takes action. Fugitoid knocks out Stockman and closes the vials. "I can fix everything" says Fugitoid.