From Sylar's native Universe (henceforth referred to as Heroverse), Sylar has access to Micah Sanders, a technopath, with the ability to communicate with and control computerized devices.
Using Micah's technopathy, Sylar could then easily hack into Cerebro, the Bat Cave's computer, and Tony Stark's personal system. This would give him virtually all of the information he needed to concoct a master plan, that would allow him to systematically conquer each Universe.
He would begin by waiting for an opportunity to catch Multiple Man alone and away from his team. Sylar would easily defeat him and steal his power.
Next he would wait for an opportunity to catch Nightcrawler alone and away from the X-Men (or Excalibur, or X-Mansion or X-Whatever), and with his telekinesis, he would eventually be able to defeat Nightcrawler, cut him open, and duplicate his power.
Now, with his powers of teleportation and duplication, he would attack Sue Storm, the Invisible Woman in a similar way, waiting until she was alone and out of reach of the Fantastic Four. With his teleportation (from Nightcrawler), duplication (from Multiple Man), telekinesis, "shapeshifting" and healing factor (the last three obtained in episodes of Heroes), he would have to kill her immediately before she could fight back, but he could do it, and he could then absorb her power of invisibility.
Using teleportation, duplication and invisibility, Sylar could then defeat Quicksilver and obtain super-speed.
Using all of his new power, plus Quicksilver's speed, he could then defeat the Flash, gaining extra super-speed and access to the Speed Force.
Now, he would begin to target the "intellectuals," people with abnormally enhanced metal capacities, such as the Leader, Beast and Forge.
At this point, with telekinesis, a healing factor, shapeshifting, duplication, invisibility, teleportation, enhanced super-speed and an enhanced intellect, Sylar should be able to defeat Magneto--the battle would be akin to Magneto fighting the Dark Phoenix alone, in my humble opinion, not much of a chance, even for the awesome Magneto.
After obtaining Magneto's mastery of magnetism, defeating Cyborg should be no problem. Additionally, Sylar could use his technopathy, magnetic control, shapeshifting and healing factor to physically steal Cyborg's cybernetic parts and make it a part of his own body--and leaving what little organic parts Cyborg actually has left to die and rot.
Now, with all of his aforementioned powers, plus his new cyborg powers, defeating Ultron and incorporating its intelligence into his own system would be the next move.
The next logical step after that is defeating Brainiac and incorporating its intelligence into his own as well. At this point, we feel that Sylar wouldn't even have to fight, he would simply let Brainiac capture him, and then use his technopathy, Cyborg's system's and Magneto's magnetism and Ultron's intelligence to simply overwhelm Brainiac, in whatever form it takes.
At this point, Sylar is ready to make his first, truly epic victory, one that will sway things almost unstoppably in his favor.... He attacks the X-Men.
His first target is, obviously, Rogue, whom he had his eyes on this entire time. The one person he can find with a more powerful absorption ability than his own. With his newfound cyborg strength and body (which he could use to encase himself in metal, avoiding Rogue's own mutant power), as well as a super-enhanced intellect, plus telekinesis, healing factor, shapeshifting, duplication, teleportation, invisibility, enhanced super-speed, as well Magneto's power, Sylar defeats Rogue surprisingly easily, and cuts her open to steal her power, right in front of Gambit and the other X-Men. From there, Sylar easily overpowers the rest of the team, and uses his new, enhanced absorption powers to not only steal their powers, but also their knowledge, memories and experience USING their powers. Sylar absorbs Professor X, Cyclops, Jean Grey, Storm, Gambit and Colossus--interestingly, by absorbing Colossus's ability to become a living metal, he can now use his shapeshifting abilities to better merge with his machine parts. Additionally, he absorbs Wolverine's healing factor, enhancing his own, but can also use his shapeshifting and enhanced healing factor in conjunction with Magneto's and Colossus' power to also steal Logan's adamantium skeleton and make it a part of his own body.
Now, Sylar goes after the high-level intellectuals, using his new Rogue-like absorption powers to add their genius to his own. Mr. Fantastic and the Fantastic Four, Dr. Strange, Lex Luthor, Deathstroke even Spider-Man are all defeated by Sylar next.
After that, he begins ramping up his game and going after some heavy-hitters, like Parasite, Abomination, Doomsday, Power Girl and The Guardian.
This gives him the strength and power he needs to defeat the likes of Dr. Fate, Captain Marvel/Shazam and Wonder Woman.
Next comes the Avengers, namely Vision and Thor. Note that Sylar, with his enhanced absorption, could most likely grab hold of Thor and absorb his power, and not let go until he has it all... meaning Sylar, for all intents and purposes would BECOME Thor, and thus become the only other person to ever wield Mjolnir.
Now would be a good time to defeat and steal the Power Cosmic from the Silver Surfer, so Sylar does so.
I could relist all of Sylar's powers again here, but it shouldn't be hard to believe that at this point he could defeat the Hulk, and absorb his ultimate strength.
Next Sylar defeats and absorbs the powers of Captain Atom and the Martian Manhunter.
After that, he defeats the Green Lantern, but must use his shapeshifting and healing factor to literally steal Hal Jordan's ring finger, tricking the ring into believing it still serves a worthy host.
Now to wrap things up, Sylar challenges and defeats the titans, such as Apocalypse (whose strength, shapeshifting, and intellect are already outmatched by the near all-powerful Sylar, at this point), Darkseid (whose Omega Beams can be replicated by Sylar already, using Cyclop's optic blasts, Captain Atom's nuclear powers and Jean Grey's telekinesis), Galactus and Thanos.
Last, but not least, Sylar has simple Kryptonite bullet ready for Superman, which he learned of from Batman's files on the weaknesses of all of his fellow superheroes. Any resistance Superman would give Sylar as the Kryptonite bullet weakens him could be easily overridden by Sylar's immense capabilities.
Speaking of Batman, Sylar purposely left Bruce Wayne and Tony Stark alive until this point, for multiple reasons. First, they are both mere humans, with no actual super powers--Sylar has no need for Iron Man's suit (which he couldn't use anyway), nor has he a need for any of Batman's Bat-toys. Secondly, be it out of arrogance, or a simple miscalculation, Sylar underestimated Bruce Wayne's and Tony Stark's intelligence, and thus never targeted them during his attempts to expand his intellect by absorbing other great minds. Thirdly, even though Bruce and Tony, together, is probably the greatest intellectual team-up of heroes, EVER, they are both still literally powerless against the man who killed Superman.
Sylar fires a blast of energy at Stark and Wayne, casually attempting to kill them both, but Iron Man sacrifices himself to save Batman, absorbing Sylar's careless attack into the reactor in his chest, killing him almost instantly.
As Batman clings to life, shocked that he and Superman and every other hero and villain failed to stop Sylar, he sees a blue, naked figure appear out of nowhere as his vision starts to fade to blackness.
Dr. Manhattan appears before the all-powerful Sylar, and calmly tells him that everything he just accomplished was in vain. Undaunted by yet another victim to defeat, Sylar attacks, grabbing hold of Dr. Manhattan and attempting to absorb his power. Dr. M. allows this to happen, and the exchange of power between the two beings annihilates both of them out of existence....
Meanwhile, back in Heroverse, the "original" Sylar sits comfortably in his home, and frowns as his duplicate is defeated in the DC Universe. Before he can send more duplicates of himself out to finish the job, Dr. Manhattan appears floating in the middle of the room in front of Sylar. Dr. M. indifferently explains that he "saw" Sylar's actions across the possible realities from his own native Universe, and that he waited to intervene until now because he had hoped Sylar would come to make the right choice and stop his conquest of the Multiverses.
Meanwhile, a duplicate of Dr. Manhattan travels back in time to the moment Sylar's parents met, and he conjures a simple coincidence to prevent it, effectively wiping Sylar from existence. However, in the present, as Sylar fades from reality and begins losing his powers, he tries desperately to fight against Dr. M., but as his powers fade, so do his chances. In a rare display of mercy, Dr. M. prevents Sylar from disappearing forever, and instead takes away every last one of his powers, leaving Sylar completely and totally human. Sylar is left alone in the Heroverse, cursed to live as "the man who should never have existed."
EPILOGUE: Years later, after Sylar mentally recuperates from his ultimate defeat, he uses memories of the-past-that-was-erased to manipulate the characters of the Heroverse into once again living out nearly the same storyline, except this time, he is merely human. However, when Dr. Suresh invents the serum that activates/grants superpowers to humans, Sylar could possibly get his powers back, and once again start the whole entire cycle over again, except this time....
Sylar is once again confronted by Dr. Manhattan after having killed off virtually every notable character in the two Universes. This time, he merely states that Sylar was given a second chance, but squandered it, and mercy was obviously undeserved in this circumstance. Just as with before, Dr. Manhattan manipulates space and time to remove Sylar from it completely, without any hope of ever returning... unless Dr. Manhattan himself wishes it.
THE END
...So, yeah....
That is how I (and my friend Mark) believe things would unfold if Marvel, DC and Heroes had a "What If/Elseworlds"-style crossover.
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