Spider-Man: Kizuna

On Marvel Earth, Spider-Man joins forces with the Avengers to battle Doctor Doom in New York City, but when several civilians are killed in a building collapse as a result, Spider-Man becomes demoralized and finds himself whisked away in a strange spacecraft called the Interdimensional Train. Doctor Doom stows aboard and both find themselves in the Tokyo of the Ultraman universe! Witnessing Ultraman battle a giant Kaiju, Doom craves the Giant of Light’s power and joins forces with Alien Mefilas and his army of Kaiju from the Monster Graveyard to steal it. (Source: Tsuburaya Productions)

A high school student named Yu Komori is bitten by a radioactive spider, which gave him spider-like powers.

In the year 200X, a supervillain who goes by the name Lord Gokibu wants to steal the fossil of the Insect King, 15 year-old Shou Amano uses his new spider powers to become Spider-Man J, to prevent this from happening. During his time as a superhero, he meets Japanese versions of Elektra, Dr. Doom, Blade, and the Fantastic Four.

Yu’s new high school is kind of awful. He’s failing his classes and striking out socially. Everything changes when he finds one of Spider-Man’s costumes abandoned in an alleyway. At first, it’s fun to put on the costume and play hero, but when powerful enemies appear, Yu quickly realizes he’s out of his element. Still, with the real Spider-Man nowhere to be found, the city needs someone to save it… (Source: VIZ Media)

The manga's story begins when iconic villain Doctor Octopus falls into a coma. When he awakens, he finds himself inhabiting the body of Japanese middle schooler Otoha Okutamiya.