In Star Trek Beyond, the alien commander who attacks the USS Enterprise is Krall.
Krall leads a large swarm of small attack vessels against the Enterprise during a rescue mission near the uncharted planet Altamid. The swarm overwhelms the starship, forcing the crew to abandon ship and separate across the hostile world.
The commander initially appears to be an alien warlord with a deep hatred of the Federation. As the story develops, his identity is revealed to be Balthazar Edison, a former human Starfleet captain. Edison was stranded on Altamid after the destruction of the USS Franklin and was transformed by the planet's technology and biological resources.
Edison had served in the Earth military before the Federation existed and viewed the Federation's principles as a betrayal of the sacrifices made by earlier soldiers. His conflict with the Enterprise crew is therefore tied to the Federation's expansion and his resentment of its ideals. Star Trek Beyond was released in 2016 and directed by Justin Lin.