The first Eon to appear is an alternate version of John, who was traveling through the dimensions to enslave other John variations. He arrives in Dimension 1, where he encountered John Smith and John 10,000. The two manage to damage the Hands of Armageddon, his main form of transportation, and killed him.
This Eon is created much later, when Intellectuary uses a Puppet John to give life to Eon, making him whole. This gave birth to this Eon, revealing to being the corrupt John from Dimension 1.
Eon 2 is a Ninja John, from the Naruto Dimension also known as Dimension 12. He is a member of the Akatsuki, and is mutated into this form after meddling with Forbidden Time Jutsu. He has control over time, and can take control of others by encasing them in a special membrane. While he is thought to have been defeated in this dimension, he is in fact thrown into the Lanes Between, serving the Chaos Lord. He gathers John variations to sacrifice one to Chaos Lord, so the Fell One would possess his DNA. Eon is the one who's thrown in instead, and is killed.
Eon 3 debuted in the John Smith 10 and Ahmad 15 crossover. This Eon possesses the Neontrix, a device that allowed him to control the Omnitrix transformations of others. He is eventually defeated and destroyed.
He is confirmed returned in Ryder 10, where he finds out about Paradox's past and him gaining his powers. He attempts to kill a powerless Paradox, but is stopped by Ryder. He uses Gutrot to erase his memory of the recent events.
He captures Paradox while powerless, cutting off his hand. John fights him, but he manages to get the Chrononavigator in the past, almost allowing Gaia to worm into other dimensions. John stops him, and uses Gutrot to erase his memory, again.
