The Heart of Darkness is a black hole generator created by Professor Zayton Honeycutt as a power source. He sold it to Kraang Subprime for a large payment, who subsequently had the Kraang use it to destroy the Triceraton Homeworld. The surviving Triceratons then took the technology for their own to be used against the Kraang.
In Earth's Last Stand, the Fugitoid sacrifices himself to destroy the Heart of Darkness.
- Annihilation Earth! - The Triceratons used the Heart of Darkness against the Earth to ensure the demise of all Kraang hideouts on the planet. Master Splinter nearly stopped it, but Shredder betrayed and killed him, thus allowing the Earth to be swallowed up into a black hole.
- Beyond The Known Universe - Many years ago, the Utroms broke up the black hole generator into three separate parts and hid them in the safest parts of the galaxy they could find. Zayton Honeycutt takes the Turtles, Casey Jones, and April O'Neil back in time six months to find the parts to change the Earth's fate.
- Riddle of The Ancient Aeons - The Utroms were revealed to have entrusted a fragment of the Heart of Darkness to the Aeons. The Triceratons were successful in claiming the Heart of Darkness fragment.
- The Arena of Carnage - The Turtles, Professor Honeycutt, April and Casey catch up to the Triceraton Flagship to steal the first fragment and sneak aboard, but the Turtles are captured and forced to fight while The Fugitoid was taken prisoner, leaving Casey and April to do it. They succeed, meet up with the others who escape thanks to Zeno, and make it to the Ulixes, successfully claiming the fragment of the Heart of Darkness.
- The War for Dimension X - The Turtles and the Fugitoid go to Dimension X to seek the aid of the Utroms to locate the remaining fragments. Though the Utroms believe the device could not be destroyed, Honeycutt assured the Utrom Council that he had a plan to destroy the Heart of Darkness once and for all. After helping the Utroms rescue their Queen from the Kraang, the Utroms provide the locations for the remaining two pieces of the black hole generator.
- The Cosmic Ocean - The Turtles and the Fugitoid head to the cosmic ocean of Varuna where they obtain the second fragment of the Heart of Darkness from the Daagon while keeping Lord Dregg and Armaggon from obtaining it.
- Trans-Dimensional Turtles - As the Ulixes travels towards Magdomar, Raphael questions why not destroy to the two pieces they possess and leave the third alone. Donatello refutes that if the Tricerations reach the final fragment, they might reverse-engineer it, hence why they have to get it first.
- Revenge of the Triceratons - the Triceratons attack the Ulixes and take the 2 fragments.
- The Ever-Burning Fire - The Turtles attempt to obtain the final fragment from Tokka, only for Dregg to steal it and offer it to the Triceratons, who then combine it with the other two to recreate to the Heart of Darkness. Then, Mozar contacts the Ulixes to notify the Turtles that they're gonna use the device on Earth.
- Earth's Last Stand - It's revealed that the Heart of Darkness was originally invented by Professor Honeycutt as an energy source, but the Kraang bought it from him and made it into what it is today. It's also revealed that the Heart of Darkness can only be destroyed by a mix of fusion and dark matter. The Triceratons set its timer up on Earth like before, but Leonardo manages to stop it at the last second. Lastly, Fugitoid takes it with him in a sacrifice to destroy the Generator for good, taking himself and the Triceratons with it.
The first fragment: Xaava-Dal
The second fragment: The Cosmic Ocean of Varuna
The third and final fragment: The lost world of Magdomar
- The device was never referred to as the "Heart of Darkness" by the main heroes; they only ever called it the Black Hole Generator.