In my write-up for
Amazon #1 (April, 1996), I went into a lot of detail about how the Amalgam Comics characters were not always, or even often, equally divided portions of two characters combined.
Mister X is a perfect example of this, because he's almost wholly the Martian Manhunter, but combined with... stuff. The simplest equation is J'Onn J'Onzz + Professor X, which is truer of the sequel comic, 1997's
JLX Unleashed #1, but still not. You see, Charles Xavier already had a much more important role in the Amalgam Comics scheme,
Doctor StrangeFate. Marco Xavier is the X in Mr. X, and aside from shopping at The North Face over Turnbull & Asser, he was lifted whole from 1960s
House of Mystery Manhunter strips. When the Amalgam story compels Mister X to reveal his true form, he's simply the Martian Manhunter with a big "M" stenciled over his right eye and down his face. That would indicate the X-Man Bishop, but he didn't turn up until a sequel mini-series where he was amalgamated with Superman. In several Marvel Comics parallel futures, mutants are branded in this same manner, although Mister X is explicitly not a mutant himself.
We have to look to the manufactured
JLX letters column to get the real skinny. It notes, "When the rebel Skrull were driven from Mars by the Kree, one lone survivor fled to Earth. Any chance he could be the missing link to mutantkind's origin?" That doesn't entirely track with the narrative, but that skrull's role is confirmed by the book's editor. "And speaking of mysterious guys, what's the deal with this Mr. X? For years over in SLEUTH COMICS, he's been shown to be a ruthless power broker and master crook, but now he's the mutant's benefactor? Something weird has got to be up with that creep!" It doesn't sound like a villainous Mr. X would be starring in his own strip, so who exactly was he clashing with in the phony title? Was it like in
House of Mystery where J'Onn J'Onzz and Marco Xavier turned out to be each other's own enemy, and if so, why wasn't that also referenced? Was Marco Xavier someone whose identity the alien replaced, or was it a construct that was always working toward the alien's interests. If this is all still mostly Manhunter from Mars myth, when does the Marvel come in?
Like
Storm is Wonder Woman, there probably isn't a specific character that forms an amalgam with the Martian Marvel.
Super-Skrull is the most well known member of the Marvel Comics shapeshifting alien race, but the only power that he possesses that the Alien Atlas doesn't is the ability to manifest and ensconce himself in fire. Now, most Skrulls just change their form, without the invisibility, elasticity, telekinesis, super-strength, or human torching. That last one is pretty key, and also, Mister X doesn't seem to have any of the personality or personal animosities of Super-Skrull. There are other Skrulls with exceptional powers, but are so obscure that they wouldn't rate an amalgamation with a Magnificent 7 member. Sadly, the Amalgam J'Onn J'Onzz is probably just
Skymax, also known as the Skrullian Skymaster, who comes from the same parallel reality as the Squadron Supreme. Yes, Martian Manhunter rates so little consideration that they just made him the analogue of himself from the knock-off Justice League.
I've devoted so much space to the Mister X mystery (or lack thereof) because
JLX #1 is mostly a plotless slugfest peppered with false continuity relations that I spelled out in
JLX in The Amalgam Age of Comics: The DC Comics Collection (1996). The New Blood mutant members of the Amalgam JLA break their framed fellow Mariner out of jail, and the core Judgment League Avengers pursue them in the opening splash of the one-shot. It spoils the comic, frankly. Captain Marvel especially looks so good that I want to read the adventures of the JLA, not their genejoke off-shoot. As with Mister X, the JLX characters are largely bereft of any imagination or effort. Firebird and Mercury at least look like their DC counterparts, but everyone else appears (and more importantly acts) like the X-Men, in a story that reads like an X-Men comic. Mister X functions like Professor X, relying on his telepathy to communicate with and command his JLX. One nice swerve is that the combination of The Angel and Hawkman has been hiding his mutant status from the JLA, but Mr. X blackmails him into throwing a fight to give the JLX an advantage. They use the distraction to escape to Poseidonis in a leaky sub, where they are confronted by Will Magnus and his Sentinels. In that undersea battle, Rogue-but-brunette is nearly crushed to death, and Mister X has to assume his Skrull form to save her.
The alien has been revealed to friend and foe alike. He explains, "I am J'Onn J'Onzz. I am the last survivor of the Martian race known as... The Skrull. I have been hiding on your world for years with the aid of my shape-shifting powers. I know what it's like to be an outcast... alone. When I learned of mutants and their persecution, I saw a wrong that needed to be righted. And, too... I saw a community, one that might be mine... a place I might belong... at last." Not-Cyclops questioned why a non-mutant should lead the team, but Substitute-Mariner called out the bigotry and welcomed the help. Mister X's commitment to finding the lost birthplace of mutants probably didn't hurt. "Somewhere in this city there must rest the secrets of why the Atlanteans departed... and where they've gone. Follow me, and I will do all I can to help you find them."

"A League of Their Own" was written by Gerard Jones and Mark Waid, drawn by Howard Porter and John Dell. The disgraced
Martian Manhunter: American Secrets was less than half a year away from getting the 1987 volume of
Justice League America cancelled. He actually wrote several Amalgam Comics, despite being very near the end of his mainstream comics career, and having had the entire Green Lantern line taken from him. It really makes you question how much the Big Two were invested in the Amalgam books. Mark Waid helped Jones on most of his books, and was five months out from co-writing
Justice League: A Midsummer's Nightmare, the book that made me build this blog. He would also often fill in for Grant Morrison on the relaunched
JLA, and Waid eventually succeeded him on that title. Porter & Dell were the artists on that blockbuster success, which takes me back to that JLA splash page.
JLX was one of the more popular and better selling Amalgam Comics, on the same glossy stock with similar coloring as
JLA. Whether this was a trial run on what DC was planning for the future, or the template upon which it was built, it seems to me
JLX was a harbinger in ways (even the abbreviated title) no one could have expected (and few seem to recognize today.) This is a literal pivot point from the creators and characters that were failing the franchise to those that would define it as a powerhouse property for the world in the coming months. That splash represented the book that I wanted to read, and would get to in 1997.