If you take the time to see how the strengths and weaknesses of these characters match up you realize that, oh, wow, the Manhunter should have either stayed home or decided to actually limit his hunting to men.
I want to show something very important to everyone, and it is listed in MM’s DC database entry under weaknesses:
Psychic Pyrophobia: The Martian Manhunter has a psychosomatic fear of fire. It is unknown what the source of this fear is, whether it is a personal fear or a cultural fear, but whichever it is, it is a paralytic fear with the Manhunter. Exposure to fire, causes him to lose his powers, and in the case of extreme fire, to lose his control over his biomorphic form. The Manhunter is more vulnerable in this form and can take damage in this vulnerable state.
He is now invulnerable to flames unless they are "flames of passion" or of some other "psychic significance."
So, while he was gotten over his fear of flames in general, he still has a weakness to passionate “flames of psychic significance.” Why . . . that sounds a lot like:

Seriously, anyone whose weakness is psychic flame has absolutely no business fighting Phoenix, a universal nexus of PSYCHIC ENERGY that manifests itself as a gigantic bird made out of COSMIC FIRE. Phoenix is nothing less than the GOD of the specific thing Manhunter is weak against. This is like someone whose weakness is thunder fighting Thor, or someone whose weakness is bacon fighting George Berryman’s refrigerator.
It’s especially crippling when you consider how this weakness affects Mr. Manhunter. He experiences paralyzing fear and LOSES HIS POWERS. Losing your powers, in this fight, is instant death. Phoenix has absolute mastery over all matter and energy, so if Manhunter loses his ability to defend himself using superhuman means then he will be atomized without resistance.
I could almost rest on that point alone, but I won’t because I want to dig the knife in deeper. Someone might say Martian Manhunter could take steps to avoid the psychic fire. He is an intelligent combatant after all. I’ll give him enough of a benefit of the doubt to assume he can stay in this fight for a while, feebly trying in vain to survive and (HA!) do damage on Dark Phoenix.
Maybe he’ll stay far enough away from the fire that the fear does not affect him, right? Well, that would leave him with ranged attacks as his only means to harm Dark Phoenix. His “martian vision,” with the power of 1000 pounds of TNT, is deeply unimpressive compared to Dark Phoenix’s planet-busting level of telekinesis. Martian Manhunter’s best bet is attacking with telepathy, but even his best bet is a bad bet. MM has very strong telepathy, I’ll give him that. It is not stronger than Dark Phoenix’s, though. The Phoenix Force is the nexus of all psychic power in the universe. She can literally draw upon the mental power of every mind that exists. Any one mind, no matter how powerful, will inevitably bend and break under such a practically limitless level of cosmic psychic force.
Incidentally, another one of Manhunter’s limitations is that his psychic powers do not work on insane minds:
Telepathy: The Martian Manhunter is the most powerful telepath on the planet[18], and is one of the strongest telepathic beings in the Universe. He is able to read the mind of any human with no difficulties, and the only minds that can cause him trouble are insane minds.
Again, wow, Manhunter is screwed. Dark Phoenix is both a superior psychic AND utterly mad, making all the effort Manhunter will spend trying to break through her psychic defenses a waste of energy. Even if he can somehow touch her mind, the second he does he will find it impossible to affect and he will in all probability be overwhelmed by the single most encompassing case of cosmic insanity he has ever encountered. Dark Phoenix, on the other hand, has no such limitation when it comes to breaking very orderly minds like Manhunter’s.
Dark Phoenix’s telekinesis also makes her a more dangerous opponent at a range than Manhunter. Dark Phoenix can affect matter at a subatomic level. Even though Manhunter can control his own matter at the
molecular level, merely being able to control molecules gives MM no way to reconstitute himself once Dark Phoenix breaks his molecules apart into subatomic particles. I think in an old fight I argued that Apocalypse could use molecular self-control as a defense against Sersei’s atomic-level matter control because he could keep his molecules in a state of flux, making it harder for Sersei to mentally latch on to the atoms those molecules comprise. But that is different because while Apocalypse was powerful enough in comparison to Sersei that he could conceivably fight effectively while still keeping his molecules in a state of constant flux, MM does not have the luxury of budgeting any of his mental concentration away from maintaining telepathic shields against Dark Phoenix. At best, MM could effectively maintain his mental integrity against Dark Phoenix, or his physical integrity, but not both, given that Dark Phoenix is godlike in both respects.
I’m trying to anticipate any other arguments. Hmmm. In his last fight, much was made of Manhunter’s phasing ability. I do not think that is a major factor on this fight because mental energies are going to be in play rather than physical attacks. If Manhunter’s intangibility somehow places him out of reach of Dark Phoenix’s telepathy, it will also put Dark Phoenix out of the reach of Manhunter’s telepathy. In order to actually fight, Manhunter will have to go tangible eventually, at which point Dark Phoenix would instantly transmute Manhunter into electrons or melt his brain, depending on where MM would want to allocate his defensive concentration.
For the sake of completeness and sheer sport, let’s indulge in the counterfactual possibility that for some reason MM is not affected by Dark Phoenix’s psychic flame and can get close enough to Dark Phoenix to engage her physically. He still loses. In terms of speed, they are either equals or Dark Phoenix is faster. Dark Phoenix could traverse interstellar distances (i.e., multiple light years) in mere moments, meaning she was moving at either hundreds or thousands of times faster than the speed of light. In terms of durability, I can’t see MM being able to do much damage by hitting her. Dark Phoenix survived diving into the heart of a star, which means she withstood, without even showing mild discomfort, pressure of around five billion TONS per square inch (if the Earth’s sun is representative). There’s no way MM’s fist packs five billion tons. Even Thor’s strength level is “only” at being able to lift
millions of tons, and Martian Manhunter is not thousands of times stronger than Thor. He just isn’t. In other words, there’s no way MM could even tickle her with physical attacks.
I’ll concede that Phoenix won’t beat MM by punching and kicking him either. Instead, she’ll win with her deity-level matter/energy/mind manipulation. This is a cosmic curb-stomp.
