The Martian Manhunter leaves the JLA in this story entitled, "And So My World Ends!" The story begins as Diana Prince (formerly Wonder Woman - but who has now lost her powers and is on leave of absence from the JLA since #69) and her mentor Ching are visiting a local carnival. Suddenly a man in overcoat and hat goes berserk, knocking over the fire eater show. Diana uses her martial arts to attack the man, but he brushes her aside effortlessly. Still in posession of her JLA signal device, the former Amazonian calls for help. In no time it arrives in the shape of Batman and Green Arrow. Thier orthodox efforts meet the same end as Diana's until Green Arrow sends a phospherent arrow, the head of which bursts into flame. At that moment the man sinks to his knees, and Batman removes the man's hat to reveal none other than the Martian Manhunter!
Back at JLA HQ, Jonn tells the story of his homeworld. Before being called to earth in the accidental experiment that began his super-heroic career, Jonn Jonzz was a Military Scientist on Mars, where he directed the forces of the Desert Dwellers in a Civil War against the Pole Dwellers led by Commander Blanx. Both sides were struggling for control of the Blue Flame - the only source of heat on Mars: Jonn to use if for good purposes, Blanx for evil. Blanx and Jonn met face to face in hand to hand battle, only for Blanx to double cross Jonn and have henchmen waiting for him. The victorious Blanx ordered Jonn to be exiled for 13 years and at this point the Martian Manhunter was teleported to earth.
His time of exile recently elapsed, Jonn returned to Mars to find a landscape of charred ruins - a once mighty civilisation had been destroyed. Jonn discovered that Blanx had found a way to get the Blue Flame to burst its bonds - therefore allowing it slowly engulf the whole of the planet Mars!
Jonn tried to lead his people in building a space craft to fly themselves to safety. Returning to earth to find some helpful materials, he suddenly felt a stabbing pain in the brain, causing him to run amok. The JLA agree to go to Mars with Jonn and Green Lantern provides transportation.
Just before they arrive, they encounter a hostile alien spaceship, which bathes them in a burst of radiation. Only Green Arrow remains conscious - because he was shielded by Superman - and the emerald archer uses his skills to fire a shaft into a nearby satellite and pull himself and Superman to safety. The Man of Steel then rescues the other Leaguers.
Superman and Green Lantern try to stop the Blue Flame from spreading while the rest of the JLA try to find a way into the alien spacecraft. The shrinking and vibratory skills respectively of the duo do the trick. The stunned aliens are soon over come by the JLA pair, and the Atom opens the portal to allow the rest of the League inside. In no time, the JLA have taken total control of the spacecraft, but the one person they really want - Commander Blanx - has departed in an auxillary rocket.
Superman and Green Lantern deduce that the only way to stop the Blue Flame from spreading is to digout the section of the planet that is burning and throw it into deep space. Their mission accomplished, the two heroes are relieved to see the rocket designed by the Martian Manhhunter set off and carry at least some of his people to safety.
Martian Manhunter then follows Blanx to the surface of the planet in what both men know will be a battle to the death. Blanx tells jonn that he made a deal with an alien race whereby they would buy Mars for its mineral wealth - but only if the whole race (apart from Blanx) were destroyed. As the two natives from Mars slug it out, Jonn hurls a huge boulder at his opponent, delivering a fatal blow. The JLA try to comfort their distraught comrade by telling him that some of his people escaped in the rocket he designed. Although they try to persuade him to return with them, the Martian Manhunter feels he must find his people and help them make a new start. Thus, the JLA and the Martian Manhunter bid one another farewell.