Where do we even start? Like the earlier X-Men: The Animated Series, this show is filled with overt and subtle references to the comics. In fact, too many episode plots or characters to list are lifted directly from the comics.——
- J. Jonah Jameson funding the creation of the Scorpion? That's actually how it happened in the comics!
- Felicia Hardy gaining superpowers as the Black Cat because of the Kingpin is actually lifted from the comics — but tweaked, in that comic-Felicia voluntarily asked the Kingpin for the power boost, whereas here she is forced into it. Additionally, comic-Felicia's initial powerset was the ability to inflict bad luck on others around her, and Spidey eventually had her Depowered against her will because her powers were constantly on and affecting those around her even when she didn't intend it; in the show, she is instead able to voluntarily shift into a form with enhanced strength and agility.
- Alistair Smythe was also mutated into the biomechanical "Ultimate Spider-Slayer" in the comics, although there it was a voluntary upgrade on his behalf, whereas in this series, he is forcibly mutated into it.
- The design of the Spider-Slayers on multiple levels. The "Mega-Slayer", a giant robot with an electronic visor that broadcasts the controller's face used in several late series episodes, is based on the Mark XIV Spider-Slayer from the comics, which was the most refined iteration of the "traditional" style of Spider-Slayer, which were humanoid robots with two-way video-screen faces. The three Spider-Slayers seen in season 1 — the Black Widow, Tarantula, and Scorpion — are based on the Marks XV, XVI and XVII from the comics. Even their conjoined form also appeared in the comics as the Mark XVIII.
- When Peter gets the Symbiote costume, he decides to test his strength by lifting a fire engine. He then remarks, "And I used to have trouble lifting a Volkswagen!" In Spidey's origin story in Spider-Man and His Amazing Friends, Peter tests his new spider strength by lifting a Volkswagon, straining a little.
- The second season, Neogenic Nightmare, is fundamentally an extended reference to "The Six-Arms Saga", a 3-issue mini-arc that ran from Amazing Spider-Man #100-#102, where Spider-Man developed six arms as a result of taking a formula intended to remove his spider-powers that instead increased them. The major change is the climactic two-parter, which sees Spidey's mutation advance until he is transformed into a near-feral inhuman beast called "Man-Spider".
- Morbius actually debuted in comics during the Six-Arms Saga, which is why he debuts in season 2 and is integral to the overarching story.
- The Man-Spider form that Peter Parker assumes after his mutation accelerates actually first appeared in an obscure Spider-Man/X-Men crossover story that ran in the first three issues of "Marvel Fanfare" in 1982.
- Whilst the "Six American Warriors" historical team from season 5 never existed in the comics, all five members who aren't Captain America are actually real Golden Age Marvel characters!
- The Black Marvel was a Badass Normal white man who received his superhero identity from a Blackfeet Native American tribe he befriended—while he did join a super-team during World War II, its identity is unknown and it never happened during his own stories. For an added Mythology Gag, the "fake" Black Marvel in this series, Dan Lyons, is named after the actual comicbook Black Marvel.
- The Whizzer gained his Super-Speed by being injected with mongoose blood as an experimental cure after being bitten by a cobra, although it was later retconned that he was a latent mutant and this simply activated his powers. He actually fought on a number of American super-soldier teams.
- The Thunderer was an American patriot who used a costume with a voice-amplifying techno-collar and a blinding light-generating "lightning gun" to stun and disorientate his foes.
- Miss America gained her powers of Flight, Super-Strength and Super-Toughness from being struck by lightning and surviving — though, like the Whizzer, this was also later retconned as her being a latent mutant. She was a common teammate of the Whizzer, and in fact actually married him.
- The Destroyer of the comics most closely resembles his counterpart in the series, having gained enhanced physical abilities ala Captain America from a prototype Super Serum, although in his case he received it from a non-Nazi German scientist whilst he was a journalist on an investigative mission to Nazi Germany. He operated behind enemy lines for the duration of the war.
- The "Secret Wars" and "Spider Wars" arcs in season 5 are, of course, references to the Secret Wars and Clone Saga events from the comics.
- Madame Web, whilst ultimately revealed as a mysterious entity similar to the Beyonder, appeared in the comics as a mysterious psychic who appointed herself as something of Spider-Man's mentor for a short time.
- In "Spider Wars", the alternative Spider-Men are all Mythology Gags on some level:
- The Scarlet Spider needs no introduction; he was the original "Spider-Man Clone" introduced in the Clone Saga of the comics.
- The Spider-Man actor is a reference to Marvel's short-live live-action Spider-Man TV show from the 70s.
- The Six-Armed Spider-Man, besides being a Call-Back to season 2, also references What If? volume 2, issue #42, which presents a universe were Spidey never cured himself of his six arms, but instead embraced them and became a fighter for mutant rights.
- "Octo-Spidey", the Spider-Man with the Doctor Octopus arms, is actually based on a 4-issue mini-series called "Funeral for an Octopus", which spun off of "The Spectacular Spider-Man", Volume #1, Issue #221, during the Clone Saga. During this arc, Spider-Man temporarily gains control of Doctor Octopus' last set of tentacles after the Doctor is killed, only to have to destroy them when the control unit was blasted and they went berserk.
- The rich, armored Spider-Man is a three-fer in terms of Mythology Gags. Firstly, his costume; it's based on the Mark 1 Spider-Armor, a bulletproof metal suit that Spidey used to defeat the New Enforcers in "Web of Spider-Man" issue #100. Secondly, his characterization serves as a nod to another hero who is wealthy, armored, and can be arrogant. Finally, he has a giant spider-robot — a nod to the 1978 Japanese toku series, where Spider-Man piloted a Humongous Mecha named Leopardon.
- Mary Jane turning out to be a clone prior to the start of the Secret Wars arc was one of the (many) ideas pitched during The Clone Saga to end Spidey's marriage.
- In the series, Spider-Man's first public appearance is a TV show called It's Amazing!.
- When Spidey visits the little girl Tiana, she asks him about his origins, saying, "Timmy says you're an alien from a planet full of spider-people that blew up. But your parents put you in a rocketship to Earth when you were a baby!" The Shout-Out to Superman is obvious. More subtle is the reference to Timmy. Tiana is the Gender-Flipped version of a character from a famous Spider-Man story, "The Kid Who Collects Spider-Man". In that story, the boy Spidey visited was named Timmy.
- In the Grand Finale Peter visits another universe where among other changes from his own universe Mary-Jane is a shallow empty-headed party girl unlike the Mary-Jane he knows. The amusing part is the shallow empty-headed party girl was her character when she was introduced in the comics before Character Development that this show had skipped in order for her to be the Betty to Felicia Hardy's Veronica. Also, Anna Watson was much nicer to Spider-Man than in his own universe; in the comics she actually was nicer to Peter.
- In the Insidious Six episode, while posing as a medical doctor, Dr. Octopus and Aunt May are shown acting quite friendly with each other. In the comics, the two actually did have some romantic feelings for each other, and Doctor Octopus even tried to marry her (admittedly as part of a scheme) in one famous storyline.
- You might think that Spider-Carnage was invented purely for the show, but in fact Ben Reilly actually did briefly become host to the Carnage symbiote during the 4-part "Web of Carnage" arc, which occurred in "Amazing Spider-Man", Volume 1, Issue #409 to issue #412, during 1996 — just two years before the cartoon version of him came to be!
- In the fifth season premiere, the monstrous version of Spider-Man in Harry Osborn's dream looks a lot like the Doppelganger Spider-Man from The Infinity War, but lacking the extra arms.
- In both of his appearances on the show, the Punisher is specifically seeking to hunt down Spider-Man, which is a nod to how he first crossed paths with the wall-crawler in the comics.
- In his second and final appearances, Kraven mentions that his pet-name for his lover, Mariah Crawford, is "Calypso". Mariah is based on Kraven's lover from the comics, whose name there was Calypso Ezili. In their final appearance in the series, her "feral" form even looks like the villainous Haitian Voodoo priestess.
