Proto and Leonidas are two odd occurrences in the Project.  Proto is a split personality and a "Generation 0" of the Project.  When Zane was introduced and selected to the Project, his mind was broken, both mentally and physically.  Aster (at the time) used Zane's brain to gauge the Genesis Engine to his preference, as to not cause harm to the body.  The science of how this worked is something only Aster himself knows how to do and to explain.   But as far as spoken words from Aster, he has told the Council that he separated the mind from body by using deep sleep.  Proto was born as a result to take Zane's separated mind and try to transfer it into another broken (mentally) body.  While it succeeded to a degree, Aster never accounted for a close symbiotic relationship to be formed from Proto's illogical and dangerous way of life.  As noted from Aster: "The mind of our Subject and his body are two separate things, it's (in theory) possible to scan the brain's activity and copy it to another's brain.  While we have done just that...it's reactions and almost dangerous actions are becoming unknown.  For now we will sedate the Prototype...".  While Proto lingers and is still alive today, sometimes he could be considered apart of the Council (as a replacement for Crimson where needed...) much is still too unknown about how Proto could have still survived.  But regardless of the events done, he served as a base to the current and first Generation of the Project, Zane. 

Leonidas, a holder of a shard of the Emperor Souls, is not as simple to explain as Proto.  Leonidas is confirmed to be the original Emperor Soul by Proto and Zane.  But why he gave that up to Crimson is never too clear.  Leonidas was originally the first Kyng of Hanai before Crimson came to ascend it, he became a little known father figure to him when the Limit Breaker experiment took place.  Leonidas was one of the guards provided to the children of the experiment and assigned to the "Crimson Tear" group, a group of 8 children who showed the best results to take on the strain of the Limit Breakers.  Leonidas became a father figure to the group while they were separated from their families.  Before the Limiters were installed, Leonidas served as a sort of trial run and was given the task of controlling the energy output of the tools and life support of everyone in the facility.  The nickname of "Emperor" was given as a joke to him due to how such an important task was given to him.  When the breakout happened and many of the subjects were killed (while the three main escaped, those becoming Crimson, Malicore and Praxis) Leonidas was appointed to find all of them and either take them alive or retrieve the Limit Breakers, even if it meant to rip them off their bodies.