Alternative versions of the character have appeared in a number of Marvel storylines. In the Age of Apocalypse alternate setting, Bruce Banner was never exposed to gamma radiation and instead experimented on mutants to transform himself into The Thing, a being similar to the Gray Hulk. In the altered reality of the 2005 company wide crossover House of M, Bruce Banner disappears in Australia, where he befriends an Aborigine tribe, and attempts to control his dark side. When the mutant rulers of the Earth attack his tribe he retaliates, and eventually conquers Australia with the aid of Advanced Idea Mechanics.

The Earth X series featured a vastly different take on the character, one in which the Hulk and Bruce Banner have finally achieved separation. However, they still rely on each other, with Banner becoming a blind child who sees through the Hulk's eyes. In an interview in Comicology Volume I: The Kingdom Come Companion, Alex Ross said that the design of Earth-X Banner and Hulk was based on the appearance of Moon-Boy and Devil Dinosaur.

In the series Marvel Zombies, the Hulk has succumbed to a virus which makes him into an undead zombie. Although he retains his strength and invulnerability, he no longer heals, does not feel pain and now craves human flesh. The zombie Hulk's transformations are controlled purely by his appetite — after feeding, he transforms back into Banner, who is also a zombie, until the hunger returns. Banner, who retains much of his intelligence and thus guilt, has the defenders of the last human colony kill his human(ish) form.

A second Hulk appears in the reality the Marvel Zombies of the original series are teleported to, known as Earth-Z. This version's life appears identical to his core counterpart up until the events of World War Hulk. When he reaches the Moon to attack the Inhumans, he is infected and his allies killed. Hungry, he heads to Earth and begins eating people, ultimately infecting the Sentry, who sets about forming a team of Zombie Avengers to eat humanity and wipe out any competition or resistance from other heroes, infected or otherwise. Hulk later is cured of his hunger by the Zombie Spider-Man and joins his New Avengers. The team succeeds in killing the Zombie Avengers and ending their plan to eat the multiverse, sacrificing themselves in the process.

In other tales, possible futures for the character have been shown. Using a post apocalyptic wasteland as a backdrop, the Peter David written Incredible Hulk: The End one-shot features the demise of an elderly Bruce Banner leaving the Hulk as the last living being on the planet. This was a different future to that shown in David's Future Imperfect storyline. This tale also featured a post apocalyptic future but one where the Hulk has mutated into the dictator The Maestro ruling the remains of humanity with an iron fist.

In another take, The Hulk is shown to still be active in the alternate future of the MC2 universe. There, he is shown as an amalgamation of his three main transformations; He has the strength of the Savage Hulk, the attitude of the Grey Hulk, and the intelligence of the Professor Hulk.

He's also shown to have fathered a son named David by an unknown spouse.

He was later seen within the pages of Last Hero Standing, where Loki manipulated him into attacking the heroes. When he was freed of his manipulation he was critical into punishing Loki within the voided dimension that Thor banished them to live out the rest of their days.

This reality is set 50 years in the future after many of the costumed villains and criminals joined forces. The result is the death of most of the various costumed heroes and the conquest of the American. In the case of Bruce Banner, excessive exposure to gamma radiation via nuclear weapons used during the conflict render him insane and results in another incarnation of the Hulk. Banner forcibly mates with his cousin Jennifer Walters and sires a progeny that possesses average human intellect, green skin and similar powers to themselves, though at lower levels. They form the Hulk gang that rule the entire west coast of the country, a domain formerly held by the Abomination. Banner, along with his children and grandchildren, live in a collection of caves and trailers, forcing those that live on the west coast to pay them rent in order to be allowed to live. Aside from affecting his sanity, the radiation Banner is exposed to earlier alters him physically. Even in his normal state, Banner possesses at least some degree of all the Hulk's superhuman abilities. After Logan returns home and learns his wife and children have been slaughtered by the Hulk gang, he proceeds to fight and kill all of them. He eventually confronts Banner himself and the two begin to fight, with Banner initially holding his own due to his strength. Logan soon gains the upper hand and impales Banner with his claws, which angers Banner enough that he transforms into the Hulk. The excess radiation has created a different incarnation of the Hulk, one in which Banner has complete control. Banner's Hulk form, while physically older, is much larger than any previous incarnation and is several stories tall. As the Hulk, Banner eats Logan whole and believes he's killed him. However, Logan's healing factor allows him to withstand the assault and heal the injuries sustained. He eventually claws his way out of Banner's body through his back, causing massive internal injuries to Banner that end up killing him. Logan spots Banner's grandson, Bruce, Jr. and spares him. Logan takes the boy to raise in an effort to someday help combat the various villains that still rule the country.

In the Warren Ellis series Ruins, a dark flip to the Kurt Busiek tale Marvels , the accidents, experiments and mutations that led to the creation of Super Heroes and super humans, instead led to terrible deformations and painful deaths. Here, Bruce Banner's story went exactly the same with his 616 counterpart, but when he was caught in the middle of the Gamma bomb explosion, instead of transforming into The Incredible Hulk, his whole body opened up from the gigantic tumours that appeared inside it, pushing most of his organs and skull outside his body, and giving Rick Jones cancer. He didn't die, and was put in an underground vault by the CIA, codenamed "the Hulk".