In addition to his mainstream incarnation, the Punisher has also been depicted in other fictional universes, in which the character's history, circumstances, and behavior vary from the mainstream setting. In some stories, another character besides Frank Castle serves as the Punisher.
Punisher 2099
The Marvel 2099 universe follows the story of Public Eye police officer, Jake Gallows, after the murder of his mother, brother and sister-in-law. Gallows comes across Frank Castle's war journal in the Public Eye archives, and took the mantle as the new Punisher. At first he follows Frank's old code of justice, only killing those who hurt the innocent. He later loses his mind, at one point proposing murdering two people simply because they were having sex with each other. He is named Ministry of Punishment in the Doctor Doom's 2099 government. He is joined by Polly, a lab-bred humanoid who becomes his partner.
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Alternative versions of the Punisher have appeared for over three decades. The earliest examples of those alternative versions can be found within the monthly What If series. Using existing Marvel stories as a starting point, the series examined scenarios in which, for example, Frank Castle's family has not died or he had killed Daredevil in their first encounter. Other "what if" stories looked at his adventures as a new Captain America or as an agent of S.H.I.E.L.D. Garth Ennis wrote a one-off special entitled Punisher Kills the Marvel Universe where Frank Castle kills every superhero and supervillain in the Marvel Universe.
The Punisher also featured in a number of more extended looks at alternative universes and lives such as the Age of Apocalypse's Frank Castle (as a man who fled genocide to become a monk).
House of M
In the alternative universe House of M, Castle appears as a media vigilante nicknamed the "Punisher" and is recruited after his arrest by John Proudstar to join and be the other human in the strikeforce known as the Brotherhood.
A Man Called Frank
A Man Called Frank, written by Chuck Dixon, was a western themed take on the character. Castle is a cowboy during the time of the American Old West who is out for revenge to the criminals who killed his family.
Marvel Noir
In The Punisher Noir, Frank Castelione is a veteran of World War I. His wife died from cancer and his only son was never killed. Instead, Castelione is killed by Jigsaw, Barracuda, and the Russian, and his son became the Punisher, patterning himself after a radio pulp series. This version of the Punisher wears a mask emblazoned with his trademark skull, similar to Crossbones, and later has it carved into his chest by Jigsaw, while Frank, Sr., has a winged version of the skull tattooed on his chest. This Punisher fights against a criminal conspiracy controlling the entire city.
Marvel Zombies vs. The Army Of Darkness
In this universe, Frank takes advantage of the fact that the heroes and law enforcement officers are busy with zombies and he hunts and shoots down the super-villain leadership of New York City, known as the Kingpin, The Owl, and Hammerhead. Along the way he allies himself with Ash Williams, who he intends to help battle the zombie threat. When Ash sees him kill the still human criminal trio he becomes disgusted and mistakenly abandons the Punisher minutes later. This leaves Frank to be attacked and infected by a squad of zombies, causing him be at first "killed". Frank returns as a zombie and turns Ash's ally, the Scarlet Witch into one. Punisher appears in Marvel Zombies: Evil Evolution, he appears zombified along with other zombies attacking the Marvel Apes.
Marvel Knights
Marvel Knights' Punisher 2099, another take on the year 2099, featured Cassondra Castle who goes by the alias of Cossandra Natchios. She is the daughter of Frank Castle and Elektra Natchios and has a son named Franklin. When she is diagnosed with cancer, Cossandra sets out to teach her son everything he needs to know to become the next Punisher. Upon her death, Franklin chooses not to take over, allowing the Punisher title to end with his mother.
Marvel Mangaverse
In the alternative universe Marvel Mangaverse continuity, Sosumi Brown is Tokyo's Punisher, who fights the crime family of Skang Kee Ho. That family uses an Oni (Japanese demon) named Oni Yew to try to stop her, but her sister, Hashi Brown, finds out about her secret. In the process, she obtains a cursed weapon which she uses to slay the Oni and save her sister.
MC2
In the alternative-future universe of MC2, the Punisher is still active, but has moved to South America to deal with the level of drug runners there. He returns to New York after hearing of a gang war between Black Tarantula and a Maggia don called Silverback, whom he had once crippled, but now has cybernetic implants. He eventually dies in a final confrontation with Silverback.
Old Man Logan
In this alternative future series, two men who have taken up the mantles of the Punisher and Daredevil, have been captured by a new Kingpin after trying to destroy his empire along with Spider-Girl. The Punisher and Daredevil are chained to posts in a full view of a crowd at a stadium, as they are gruesomely dispatched by dinosaurs.
Ultimate Punisher
The alternative universe Ultimate Marvel version of Punisher is Frank Castle, an ex-NYPD police officer whose family was killed by corrupt police officers who knew he was going to expose them. He manages to kill the one responsible for his family's death after sympathetic cops "accidentally" place him as the man's jail cell roommate. After he unsuccessfully tried to kill Boomerang, he later kills corrupt cop Jeanne De Wolfe.
In Ultimate Comics: Avengers 2, the Punisher is defeated and arrested by Captain America. He is saved from the death penalty by Nick Fury orchestrating his release from custody in exchange for joining the Avengers. After being equipped with a Captain America-inspired costume, Punisher is implanted with a chip that delivers a violent electric shock whenever he disobeys orders. Being knocked out by Clint Barton, it allowed him to escape after the fight between two of the Ghost Riders. In Ultimate Avengers vs New Ultimates, he was incarcerated after assassinating the Russian criminal known as the Red Hammer and is later visited by Fury persuading him to rejoin the Avengers by offering him revenge on his fellow prisoners. While the Avengers were battling the New Ultimates, Punisher was aiming a sniper rifle at Captain America's kneecap with the intention of immobilizing him. However, Spider-Man swung in to push Captain America away and was hit by the bullet instead. Horrified that he had shot a kid, he begged the S.H.I.E.L.D. agents that arrived shortly afterwards to "punish him".
After Punisher and the rest of the Avengers were arrested by S.H.I.E.L.D., they took Tyrone Cash's serum and temporarily gained Hulk-like powers. They confronted the new S.H.I.E.L.D. Director Gregory Stark, but are easily defeated thanks to Stark's Nanite-based suit. The Avengers later assisted the New Ultimates against Stark's Spider in Korea. In the aftermath of the conflict, Punisher is last seen torturing the other convicts in prison.
What If
In What If...the Punisher's Family Had Not Been Killed in Central Park?, Castle's family does not die in the park and he joins the police force following his discharge from the Marine Corps. However, Frank tries to collect evidence on corrupt cops, but they attack Frank's house in the middle of the night, killing Frank's family and his brother-in-law. Castle returns to kill those who murdered his family, making Frank become the Punisher after all.
In "What If The Punisher Had Killed Spider-Man?", an alternative version of the events depicted in The Amazing Spider-Man #129, the Jackal successfully dupes the Punisher into killing Spider-Man and abandons him to take the fall in his place. Becoming a hunted fugitive, Punisher eventually hunts Warren down and intends to surrender him to the police. But when the NYPD is about to arrest him instead, threatening to kill him should he shoot Warren, Warren is executed (off-panel) by the Punisher after the latter gleefully concludes the story with the words: "See you on the other side, Jackal.".
In What If, Captain America is seriously injured in a fight with the Red Skull (an alternative ending of Captain America #212) and converted into a cyborg, which drives him to bestow his uniform upon another candidate. Castle is eventually chosen, and although he first pursues his family's killers in his usual alter ego, after a talk with the recovered Steve Rogers and some soul-searching he becomes a new and worthy Captain America.
In What If, Frank is possessed by Venom instead of Eddie Brock. With the Punisher as Venom, he goes on a rampage killing several villains including Tombstone and the Kingpin. He eventually confronts the symbiote and they work together.
In What If...Wolverine Had Become the Lord of Vampires?, Frank is chosen by the spirit of Doctor Strange to fight the vampires. Frank does so by killing Cyclops, Nightcrawler, Colossus, Storm, and Juggernaut, all of whom became vampires. When Frank fights Wolverine, he accidentally kills Kitty Pryde, causing Wolverine to kill him.
In What If features Wolverine becoming the Punisher during the 1920s.
Wha...Huh?
The Punisher appears primarily in the segment titled "What If the Punisher Was a Bleeding Heart?" in which he sympathizes with criminals and attributes their behavior to the environment in which they were raised. He is promptly shot dead.
Age of X
In the X-Men crossover Age of X, another universe's General Frank Castle commands a mutant-hunting version of the Avengers.
Marvel Universe vs The Punisher
In this alternative universe, an unknown pathogen transforms the entire metahuman population, as well as basic civilians, into homicidal cannibals. One year prior, the Punisher raided a Mafia deal in a warehouse, incidentally releasing the plague. He is one of the few people immune to the pathogen, another being the Avenger Hawkeye. The Punisher mercy-killed Captain America. The Punisher hunts for the first known infected, Spider-Man in a New York City that has been depopulated.
Castle is constantly bugged by a cannibalistic Deadpool, who he has killed over 35 times. The Thing, The Hulk, Kingpin, and others are hunted and killed. Spider-Man confronted Castle and begged for him to rescue his mate, in exchange for group of survivors . The Punisher rescued a pregnant Mary Jane Parker from the hands of a flesh-eating Kingpin and his cohorts. At the end, Mary Jane looks on aghast as Castle kills Spider-Man and sends off the survivors. Punisher stays behind on Manhattan.
Spider-Gwen
In this alternate universe, Captain Frank Castle of the NYPD is called in to take over for George Stacy in the hunt for Spider-Woman. It is also stated that in this universe, his family is apparently still alive.