Major Balthazar Edison, human, was a MACO who fought in both the Xindi War and the Romulan War. After the two wars eventually lead to the formation of the United Federation of Planets. The MACO forces, which was a branch of the Earth military, were incorporated into the newly formed Starfleet. As a decorated MACO officer, Krall was granted the rank of Captain and given the USS Franklin, the first warp 5 capable Starfleet ship of it's time. Balthazar is a soldier of war and his transition to starship Captain was not easy. He did not believe in his new mission of "exploring strange new worlds, discovering new life and new civilizations", seeing it more as Earth's way of shoving him aside. He also resented that former enemies, the Xindi, were now members of the Federation. I can only speculate on this, but it is highly possible that Balthazar was a member of the xenophobic terrorist group, Terra Prime. This is the same organization that attempted to drive all aliens from Earth in 2155 (Enterprise season 4, episodes 20 & 21, "Demons" and "Terra Prime"). As a result, Balthazar has deep reservations about the Federation. Humans did most of the hard work, fighting to push back the Sphere Builders and later the Romulans. So why should Humanity be subsumed under a vast Federation? No, all alien species should be thankful to Human Beings and be subservient to Humanity. In other words, Balthazar believes a Human Star Empire is a better model of governance than a Federation. And when Balthazar discovered this alien world hidden behind a seemingly impassible nebula, it's history, and it's technology, he decided it is the perfect staging ground. He abandons the USS Franklin, a symbol of Starfleet and wholly adopt the alien technology. With that, he begins planning the destruction of the Federation and returning Humanity to its rightful place, at the center of the universe. Now, I admit this is where things get a little fuzzy as to why he spent nearly 100 years plotting and planning. Maybe it was the alien tech, maybe it was absorbing the life of aliens. Either way, the process has warped Balthazar, turning him into Krall. It also warped his thoughts, turning Balthazar into the very thing he hated - an alien. That's what set up the chain of events in Star Trek Beyond.
We've been talking a lot about Krall, his background, and motivations in this thread if you'd like to join the conversation: http://www.trekbbs.com/threads/concerning-kralls-back-story.282362/