The Brotherhood are a race of bipedal lizards and inter-dimensional conquerors who serve as the main antagonists of the 2003 TMNT episode Trouble with Augie.
The Brotherhood travel to other worlds and dimensions so they trick the inhabitants by befriending them and eat them. However they were soon stopped by a peaceful technologically advanced race known as the Zodac, after befriending them by pretending to offer peaceful coexistence, taking over their city, and destroying their civilization, the Zodacs then disabled the transdimensional device, that was used bring the Brotherhood to their dimension, to save other dimensions from their fate and keep the Brotherhood trapped within theirs. Without the transdimensional device the Brotherhood could only serve as their conquering of other worlds came to an end.
Then April's uncle Professor August "Augie" O'Neil came to the dimension and the Brotherhood befriended Augie, whom they called the Magician, and enlisted to help repair the transdimensional device as he used ones on Earth and the dimension he was previously in to arrive in the city. They claimed the city was their and they wanted to bring their advanced technology to Earth, when in reality they intended to resume their conquest of other worlds and devouring the people, starting with Earth. Augie used transdimensional device to send a message to Earth that the Brotherhood wanted to help them, which crossed paths with April and Donatello who traveled to the city and where welcomed by the Brotherhood and taken to Augie.
While Donatello chose to explore the city he eavesdropped on the leader of the Brotherhood, the Councillor, talking to another member and learned of the Brotherhood's true intentions. After Donny warned April and Augie, the Councillor and other members of Brotherhood revealed their true colors and attacked them, but they managed to escape to a place in the city that the Brotherhood called the Forbidden Zone where the skeletons of the Zodacs where kept. In the Forbidden Zone the three learned of what the Brotherhood did to the Zodacs, and Augie vowed to not allow the Brotherhood to reach Earth. However, the Brotherhood followed to the Forbidden Zone and surrounded them. While April and Donny managed to escape from the Brotherhood, they managed to capture Augie and force to return to repairing the transdimensional device. As the Brotherhood began to assemble their army to begin their invasion for Earth, Don and April stuck back into the lab to see Augie. After Donny explained his plan to stop the Brotherhood by using the magnetic charges the Zodacs used to disable the transdimensional device, Augie tells Don it won't because he repaired the device with shielding the charges. However, April gets an idea and the three travel to the wasp world Augie traveled to before arriving in the city, with The Councillor and some warriors of the Brotherhoof following mistakenly believing the world is Earth. After Donatello, April, and Augie use the transdimensional device in the Wasp World to return Earth with the magnetic charges timed to go off and destroy the transdimensional device, the Brotherhood comes and starts looking for them. They are then attacked by the giant wasps that live in the world and end up getting killed by them.
It is unknown what happened to the rest of the Brotherhood after that, but it is presumed they eventually starved and died out, ending their reign of conquest for good.