The Legion goes to war with itself in Adventure 333 (June 1965), written by Jerry Siegel, an event so abrupt that it must reveal some long-simmering tension within the team.
It all begins innocently enough, with Phantom Girl helping out at an archaeological dig, where a plaque is discovered that refers to a war between Krypton and Earth. Saturn Girl and Superboy travel back in time to ancient Krypton, along with Lightning Lad, Colossal Boy and Element Lad, while Brainiac 5 takes Phantom Girl, Light Lass, Star Boy and Chameleon Boy back in time on Earth.
Superboy discovers a group of his fellow Kryptonians are leaving the planet to set up a colony on Earth, and his group of Legionnaires accompany them. Meanwhile, Brainiac 5’s group discovers some alien settlers who are building the city of Atlantis.
When the two colonizing parties meet, Saturn Girl and Brainiac 5 immediately start a furious argument, which quickly escalates into war. Just to be clear on this, the war is NOT started by the Kryptonians or Atlanteans, but by the Legionnaires themselves! Superboy, who ought to be on the Kryptonian side completely, is instead trying to make time with Atlantean Leta Lal, fatally attracted by her initials.
The war is, at least, a sort of peaceful one. Neither side actually wants to kill the other, although the Atlantean weapons do accidentally cause some Kryptonian deaths.
In the end, the environment determines the winner, as the Atlanteans cannot exist with the xenon in Earth’s air. Brainiac 5 artificially “evolves” them into mer-people, and Star Boy sinks their city below the water. The Kryptonians fare no better in the long run, being killed off by the giant lizards they brought from their home planet.
Although all seems well with the Legionnaires, and Saturn Girl and Brainiac 5, at the end of the story, his resentment over this may be the cause of his behaviour during the Computo story a few months down the road.