Alter Ego was created by the Stranger at the same time he created Ego the living planet. Once he created Alter Ego and Ego he gave Alter Ego to the Collector to put in his museum.
Alter Ego lived in his own private pocket universe alone, never knowing there was anything other then himself. Then one day Thor was thrown into Alter Ego's universe and Alter Ego discovered there were other beings. He escaped from the pocket universe and quickly learned there was another living planet, his twin brother Ego.
The Stranger gave him power and sent him towards his brother knowing the two would destroy each other and hopefully Earth. On the way Alter Ego ate Thor and Zephyr, and gained some of Thor's power and knowledge.
When the two planets found each other, they started fighting and Alter Ego bit his brother's eye out, but Ego used his power to destroy Alter Ego.
Zephyr used her new powers to save Alter Ego and made it into a moon for Ego. The three then left the solar system in search of the living planets new destiny, as a new family.