With the popularity of the Miles Morales: Spider-Man video game and Spider-Man: Into the Spider-Verse, many younger fans might not remember how this hero got his start. Miles Morales was a 13-year-old kid who was bit by a genetically enhanced spider and lived in a world without a Spider-Man. It was like the animated movie, but he never had a Spider-Man from another universe to help him.
Miles was a little kid who had to figure things out on his own, making his job even harder. His villains were all older, stronger, and more ruthless than anything he ever experienced. His most powerful bad guys forced Miles to use all his might and will to beat them, and there are some he never could beat on his own. These villains used their overall strength, intelligence, cunning, and experience to operate as villains no teenage superhero should have a chance to defeat.
Scorpion (Ultimate)
While Mac Gargan's Scorpion was one of the main villains for Spider-Man since he started, he never appeared in the Ultimate Marvel Universe until after Peter Parker died and Miles Morales took over as Spider-Man. In this world, he was an extremely powerful gangster and the first genuine threat that endangered Miles.
This wasn't the masked man with the big tail. This was a mob boss who was a giant man, with superhuman strength and durability, plus a healing factor. He was so powerful that Miles' uncle, The Prowler, tried to get Miles to help him bring the villain down.
C.R.A.D.L.E.
When the U.S. Government created a new law banning teenage superheroes, an organization rose that enforced the laws. This was C.R.A.D.L.E. This group was very powerful for two reasons. The first was that it had some big guns leading them, with Dum Dum Duggan called in to help.
Second, it had jurisdiction over the police, politicians, and more. They even arrested Miles Morales' high school friends who wouldn't sign a loyalty pledge and threatened a local Councilwoman with arrest for coming to their defense. C.R.A.D.L.E. is not as powerful as others because Captain America proved he could force them to back down and Dum Dum Duggan walked out on them.
Roxxon Corporation
Roxxon Corporation has been a thorn in the side of teenage heroes in the Marvel Universe for a few years now. They have made life hell for Ms. Marvel, Miles Morales, and The Champions as a team. They are also who was responsible for the underage heroes law and C.R.A.D.L.E.
They are more powerful than C.R.A.D.L.E. for one big reason. The U.S. Government shut down C.R.A.D.L.E., but Roxxon is a business corporation and as long as they keep their misdeeds hidden, they remain almost untouchable while still targeting the underaged heroes like Miles Morales.
Mysterio
Years before the Ultimate Marvel Universe ended and he joined the main 616-Marvel Universe, Miles Morales met Peter Parker thanks to a rift in the timeline. Kindred helped Mysterio find a way to get into the Ultimate Marvel Universe and killed Kingpin, taking over the underworld.
Miles Morales was not able to beat Mysterio alone, even with Nick Fury and S.H.I.E.L.D. However, soon Peter Parker made his way into the Ultimate Universe looking for Mysterio and he worked with Miles to finally bring the villain down, although it was not an easy battle.
Venom (Ultimate)
Venom was powerful in the main Marvel timeline, but there was more than one version in the Ultimate world, and both were incredibly powerful. The original was created by Peter Parker and Eddie Brock's dads and it was Eddie who took control of the symbiote and attacked Peter after their dads' deaths.
The next Venom was Miles Morales' enemy. He was a scientist named Conrad Marcus who created the spider that bit Miles, turning him into Spider-Man. He almost killed Miles and did murder the boy's mother before finally falling to the young Spider-Man, thanks to his Venom Blasts, one power Miles has that Peter Parker doesn't.
Prowler
The Prowler is Miles Morales' uncle Aaron Davis. He had a lot of power over Miles Morales for one big reason - his nephew really loved him. This led to big moments in the mainstream universe when Miles helped Prowler turn good and die as a hero.
However, he was the first real dangerous enemy for Spider-Man when Miles became a hero as a teenager. Aaron threatened to reveal Miles' secret if his nephew didn't help him become a new crime lord and it took all the teenager's intelligence to stop his uncle.
Selim
One of Peter Parker's biggest problems came when he entered into the Clone Saga. In 2021, Miles Morales ended up in his own Clone Saga. However, this was not a clone replacing Miles, it was three clones that tried to ruin Miles' life and destroy everything he represented.
The leader of the clones was Selim, and he was trying to find a way for him and his "brothers" to remain alive, knowing they were all dying. Miles destroyed their lab, not knowing he was dooming them to death. They set off to kill Miles and he had no chance of beating them. He only won when one of the clones turned on Selim and saved the original.
Doctor Doom
Doctor Doom is one of the most powerful villains in the universe, and it doesn't matter if it is Marvel's 616 or the Ultimate Marvel Universe. That put Miles Morales in grave danger when Doctor Doom targeted him. Doctor Doom wanted to know what made Miles tick and hired Hydra to capture him and bring him to him.
Doom then began to experiment on Miles, blasting him with lasers to get some tissue samples before Miles suddenly powered up. It took all he had, but Miles finally beat Doctor Doom. Sadly, this was one of the last things that Miles could do before the incursion ended his world.
Ultimatum
Ultimatum is easily one of Miles Morales' most powerful and deadly enemies for one very important reason. He is Miles Morales. This is the Miles who was born in the 616 Marvel Universe and he wanted only one thing — to get rid of the Miles Morales that came to this world from the Ultimate Universe. Miles Morales, Spider-Man, was too powerful to stop.
Ultimatum did a lot of bad things to Miles, including hiring the mysterious Assessor to experiment on Miles, and then he built a machine to eliminate his variant. It took Miles and Captain America working together to slow down Ultimatum and only when The Prowler sacrificed his own life did they finally beat him.
Assessor
The most powerful villain that Miles Morales has ever faced was a being known as the Assessor. There is no background on what this being is, only that it is all-powerful and one of the most intelligent beings in the universe. He is who helped create the clones that included Selim.
He is also who Ultimatum hired to break down Miles. The young hero never had a chance and only survived his encounters with the Assessor. It also caused Miles a severe case of PTSD and when Iron Man saw how bad Miles was hurting, he went after the Assessor and he couldn't even stop the threat. At the moment, the Assessor seems unbeatable.