The change in appearance and attitude leads to a third mini-series in 2006 from A.J. Lieberman. J’onn decides to abandon the Justice League and chooses to became a paranoid, impulsive, and harsh alien seeking a new purpose in life. By chance, it comes his way when he discovers Green Martian survivors of his world who left before contracting H’ronmeer’s Curse only to be captured by the US government and experimented upon. This, however, turns out to be a ruse by a Green Martian named Cay’an. A survivor of H’ronmeer’s Curse, Cay’an blamed J’onn for their race’s genocide by not killing Ma’alefa’ak after he killed their mother. Coming to Earth, Cay’an learned of J’onn and plotted her revenge, including kidnapping White Martians and hypnotizing them into believing they were Green Martians. This was to give J’onn a new family only to take them away again as all but one of the Martian refugees died. The survivor, Till’all, was brought by J’onn to the League while Cay’an escaped and plotted her next attack. J’onn realized he was so easily duped because of the newfound attitude he developed, realizing part of it came from the guilt of Blue Beetle’s death.
During the events of 52, another Martian would appear. M’gann M’orzz, or Megan Morse (named after Geoff Johns’ friend former Wizard staffer Ben Morse and his then girlfriend, now wife, Megan), claimed to be a Green Martian who joined the Teen Titans as Miss Martian only to leave and became a hero in Australia. She would eventually return to the Titans where it’s revealed she’s a White Martian rocketed by her parents to the Vega System before the start of the Martian Civil War (claiming to be Green because of the stereotypes associated with her race). Around this time, the Martian Manhunter would appear on television again, this time in the series The Batman. The mysterious John Jones would approach Batman and warn him of an alien race called the Joining (a techno-organic race similar to Brainiac) set to invade Gotham. When the invasion takes place, Jones reveals himself to be the Martian Manhunter and joins the battle. Following the heroes victory, J’onn introduces Batman to his Justice League (who take up the next and final season).
When Batman decided to reclaim the Outsiders in the comics, J’onn was selected to join his team. However, the addition would be short-lived when the series changed writers and the Manhunter was written out. J’onn appeared as the League’s spy on the prison planet Salvation portraying the villain Blockbuster in Salvation Run. He would be found out and made a prisoner until Libra summoned him in the pages of Final Crisis where he is executed with a flaming spear. As his final act, he imprinted the history of Mars telepathically into the minds of his closest friends. Dozens of Earth’s heroes assembled for his funeral as the Green Lantern Corps amassed as part of his burial on Mars. His peace is short-lived when a black power ring summoned the Manhunter from Mars in service of Nekron during Blackest Night. The hero is then sent to destroy his friends Green Lantern Hal Jordan and the Flash Barry Allen. At series end, J’onn is resurrected by the White Light Entity for a mission. But before that, he had to contend with D’Kay D’razz.
While Martian culture largely existed by the Great Voice, some were not open to it. Green Martian D’Kay D’razz decided to experiment on these beings only to be found out and imprisoned. When H’ronmeer’s Curse wiped out Mars’ living beings, D’Kay survived from being in solitary confinement. When Dr. Erdel’s machine reached out to obtain alien life, D’Kay was what it returned. Surrounded by so many thoughts and minds, the Martian went insane erasing all memory of her from Erdel and stealing the identity of another, assuming her life and forgetting her past. This changed when J’onn died and sent out his record to his friends. Parts of the mental barriers starting to collapse, she fully realized what she was when J’onn came back from the dead. D’Kay desperately sought J’onn out as a mate, the latter realizing she was a murderous psychopath and was forced to fly her into the sun to stop her. J’onn is then chosen to battle the Dark Avatar (a seeming Black Lantern Swamp Thing) where the Martian is turned into some earth elemental by the Entity. Swamp Thing then returns J’onn to normal.
For the cartoon series Batman: The Brave and the Bold, J’onn J’onzz was a member of the Justice League International who split his time between being a repairman, counselor, and tactician (Ma’alefa’ak appeared as a White Martian in the comic book series based on the cartoon). In the animated series Young Justice, Martian Manhunter is present but Miss Martian is a starring character. Therein, she claims to be J’onn’s niece who won a contest similar to that of Wonder Woman’s origin selected to be a representative of Mars on Earth. In truth, she snuck aboard J’onn’s ship and wasn’t discovered until he had already traveled too far for Earth. Also, while she is J’onn’s niece, she is also a White Martian which she is ashamed of because her people are seen as lower class on her world. In Young Justice, Mars is called M’arzz by its residents where there are three races: Green, Red, and White. The people live in caves because the surface is inhospitable, they communicate almost exclusively telepathically, and their government is a monarchy. J’onn also appears in the animated films Justice League: Crisis on Two Earths (where he has an evil counterpart named J’edd J’arkus after Edgar Rice Burroughs’ Tars Tarkas) and Justice League: Doom (which features Ma’alefa’ak).
Following circumstances of the comic book event Flashpoint, DC Comics saw its universe rebooted again. Among the various criticisms of the changes, a common one is a continuity best described as inconsistent (likely the Batman universe afflicted hardest). In what is being called the New 52, the Martian Manhunter was not a founder of the Justice League nor a member of the group when the reboot began. However, different books seemingly can’t decide if he was a member at some point in the past (some say yes, others say no); though, it appears his being a member won out and he left after a physical altercation with the group. Regardless, when the New 52 began, J’onn was a member of Stormwatch. An organization active since the Dark Ages combating alien threats for eons in secret, Stormwatch’s members don’t consider themselves heroes as much as soldiers. The title would change writers three times in a span of two years where scribe Peter Milligan wrote out J’onn about a year into the book’s run. For reasons yet revealed, J’onn left the group and wiped the memories of his ever being a member from his teammates. However, current writer Jim Starlin erased the team’s past existence from history which means Manhunter now has likely never even ever been a member. In any event, J’onn went on to join the Justice League of America.
Taking instructions from Amanda Waller and Steve Trevor, the Manhunter from Mars was a counter-measure against Superman as well as the Justice League of America’s field leader. In the group, J’onn develops a close relationship to Stargirl (reminiscent of that with Gypsy pre-New 52). Revealed in a series of back-up stories in the pages of Justice League of America, Geoff Johns plotted and Matt Kindt wrote J’onn’s latest origin. Selected to inherit leadership of the planet Mars, J’onn had to take part in the Test of State, a hunt for a dangerous creature on Phobos. Disconnected from his people during this time, he returned to find himself the last of his kind as the planet was engulfed in flames. A parasite on Earth named Thoth sought telepaths with its mind eventually reaching Mars. As the Martians interacted with it, Thoth consumed their thoughts and lives like a virus. Tracking it to Earth, J’onn killed its host unaware of its true nature at the time as the entity simply moved on to others unknown. These stories establish that J’onn’s weakness to fire is again psychological, this time caused from the guilt of being Mars’ sole survivor. The JLA would reshuffle in wake of the event Forever Evil by moving to Canada and becoming Justice League United, retaining J’onn, Stargirl, Green Arrow, and Hawkman.