Let's see who can kick Dr. Manhattan's (Jonathan Osterman) butt in all of DC/Marvel universes -
Dr. Manhattan vs Wanda Witch (Scarlet Witch)
Scarlet Witch (Wanda) possesses the power to modify
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Can Scarlet Witch do anything against Dr. Manhattan - Since she can change the reality itself, she can most certainly effect Dr. Manhattan's ability to attack or defend. For example, she can reduce the probability of Dr. Manhattan's reconstruction to near zero and then Dr. Manhattan will just not be able to come back from dead!
How can Dr. Manhattan kill Scarlet Witch - Again, what is working in Dr. Manhattan's favor is the knowledge of future. Since Dr. Manhattan already knows exactly what Scarlet Witch will do even before she starts to think about it, he can easily make his own "changes" to reality!
So, in essence, Dr. Manhattan can kill Scarlet Witch even before she thinks of attacking.
Further, Dr. Manhattan can teleport himself out of Wanda's range of attack before she can attack.
Verdict - Dr. Manhattan wins hands down but mostly because he can predict future.
Dr. Manhattan vs Mr. Mxyzptlk
Mr. Mxyzptlk is perhaps tops the DC super villains in terms of magical powers. Mr. Mxyzptlk is a fifth dimension elf who is not bound by our three dimensional universe's laws and therefore can mess up the reality itself and in DC universe there is no way to beat him.
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Mr. Mxyzptlk generally operates by manipulating three dimensional reality as he wishes so he can easily turn Dr. Manhattan into dust or annihilate forever. But again (at the risk of repeating millions of times already), Dr. Manhattan can rebuild himself.
How can Dr. Manhattan kill Mr. Mxyzptlk -
Dr. Manhattan can predict Mr. Mxyzptlk's arrival and attacks but it's unclear if the future will stay the same after Mr. Mxyzptlk's intervention.
Dr. Manhattan can try to make Mr. Mxyzptlk spell his name backwards. This is the only "weakness" that Mr. Mxyzptlk imposed on himself. But Mr. Mxyzptlk can come back so it doesn't really matter a lot.
The only way to really fight Mr. Mxyzptlk is to fight him in a five dimensional reality. So, the answer largely depends on whether Dr. Manhattan has access to fifth dimension or not. Given the facts that we have though, Dr. Manhattan is certainly not bound by three dimension (Dr. Manhattan is at least a four dimensional being); it's possible that he can access all eleven dimensions. If so, Dr. Manhattan can easily destroy Mr. Mxyzptlk.
Verdict - Not enough information on both Mr. Mxyzptlk's and Dr. Manhattan's full powers but if we assume the worst then the fight can last till the end of the universe
Dr. Manhattan vs "smart" superheroes (Mr. Fantastic, Lex Luthor, Tony Stark, Brainiac, Dr. Doom etc)
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Can our "smart" superheroes do anything against Dr. Manhattan - Not much. If there is one weakness that Dr. Manhattan has is a tachyon field. A Tachyon bombardment essentially takes away Dr. Manhattan's ability to predict future leaving him slightly confused. So it's possible to build Tachyon generators that slow him. But that's about it!
How can Dr. Manhattan kill Mr. Fantastic and team -
Well, Dr. Manhattan can annihilate the whole solar system, thats the easy way.
Dr. Manhattan can also track the Tachyon generators down and destroy them, thus getting his powers back.
Verdict - Dr. Manhattan wins hands down but the Tachyon attack might slow him down.
So, individually none of the strongest and smartest of DC and Marvel superheroes are a match for Dr. Manhattan. He really is probably the strongest superheroes ever created!
Keep reading next battles -
Part 1 - Dr. Manhattan vs Superman and Hulk
Part 2 - Dr. Manhattan vs Dr. Strange, Doomsday and Galactus
Part 3 - Dr. Manhattan vs Silver Surfer, Dark Phoenix and Professor X
More about Dr. Manhattan -
Zack Snyder's blunders in Watchmen - What Zack Snyder must've been thinking Part I
What Watchmen movie was missing - What Watchmn Graphic novel had but movie didn't
Read about funkiness involving Dr. Manhattan's transformation - Osterman's funky transformation into Dr. Manhattan
To find how Dr. Manhattan became so powerful, click - Dr. Manhattan's Origin and Superpowers
To find some funny details about Dr. Manhattan's personal life, click - Dr. Manhattan's personal life and his girlfriend Silk Spectre
To read some of Dr. Manhattan's memorable quotes, click - Dr. Manhattan's memorable quotes from Watchmen
To find about other Watchmen character's super powers and super craziness, click - Watchmen character's super powers and super craziness