The Marvel characters depicted in these games were often based on their incarnations in various early 1990s animated series (particularly X-Men), and were often voiced by the same voice actors.
Many of the characters and fighting mechanics used in these games were first developed and refined in two other fighting games Capcom had developed earlier, serving as precursors to the series: X-Men: Children of the Atom, which featured characters strictly from the X-Men universe, and Marvel Super Heroes, which gleaned characters from Marvel's entire roster (X-Men included).
Although the tag-team fighting concept was not new, it was refined with this series (although fans would argue whether this was for better or for worse). New fighting game terminology, such as "Aerial Rave" (the act of performing a combo on an opponent while the opponent remains airborne) and "Variable Combination" (the act of having two or more characters on the same team to perform their hyper combos at the same time) were added to the fighting game vernacular with this series.
There does not appear to be a concrete story behind each game in the series, although several plot points run across the various games of the series. However, various pairs of characters - typically one Marvel and one Capcom, were often partnered with each other during gameplay (although later games randomized the partnerships so that it was possible to complete the game facing all Marvel or all Capcom teams). There has been confirmation that in Marvel vs. Capcom 3, unlike previous installments, the subtitle, Fate of Two Worlds, will actually tie into the game storyline and plot.[1]
However, several interesting (but obviously non-canonical to both Marvel and Capcom continuities) side-plots did emerge throughout the series, some of which contradict the others:
Wolverine seeks Akuma as he believes Akuma has information about his own past. However, in order to get the information from Akuma, he must win a fight to the death.
Chun-Li was made an honorary member of the X-Men, despite the lack of mutant powers on her part. Ryu is also offered membership in both the X-Men and Avengers, but turns it down both times, preferring to continue on his own path.
Magneto and M. Bison team up, intending on betraying each other at a later time. In Magneto's ending, Magneto eventually manages to get the upper hand and kills Bison, with the Shadaloo Kings (Balrog, Vega, and Sagat) joining him afterwards, fearful of Magneto's power. The opposite happens in M. Bison's ending.
Charlie is kidnapped by Bison, who uses Shadaloo's technology to transform him to a super-soldier henchman known as Shadow.
In Marvel Super Heroes vs. Street Fighter
Apocalypse captures Akuma and turns him into Cyber Akuma.
Confirming Charlie's ending from the previous game, Shadow appears as a selectable character. In Bison's ending, a completely mechanical Charlie (built with the technology behind Cyber-Akuma) follows Bison's orders to spread fear and destruction in the name of Shadaloo.
In Omega Red's ending, he apparently kills Ryu, prompting Ken to also seek revenge.
In Dan's ending, Akuma is hinted to be his father. However, this ending, much like Dan himself, is a parody of the Art of Fighting series. In this case, the ending to the first game.
In Akuma's ending, Dan is turned into Cyber-Dan by Apocalypse. He is very easily defeated by Akuma, though.
In Ken's endings, the events of the games never actually happened. In X-Men vs. Street Fighter, he was playing the game itself with his son Mel, while the events of Marvel Super Heroes vs. Street Fighter appear to be a dream. He wakes up and continues his training with Ryu.
In Marvel vs. Capcom
When Onslaught emerges, Charles Xavier subconsciously calls the Capcom heroes to help stop himself.
Shadow turns on Bison, who then tries to subject Chun-Li to the same fate.
In Shadow Lady's ending, Jin Saotome is attacked by M. Bison and left near death. Shadow Lady and fellow cyborg Shadow find Jin and to prevent his death, they modify him into a being like themselves.
In Zangief's ending, he, in his Iron Body form, battles Jin's Cyberbot, Blodia.
An unspecified accident causes Morrigan's mind to be transferred into the body of her sister, Lillith, and vice versa. When the two attempt to return their minds to their rightful bodies, Zangief interrupts. It is heavily implied that this results in Morrigan and Zangief's minds trading bodies.
Marvel Characters
This is a list of all the Marvel characters that have appeared in the Marvel vs. Capcom series, most of which have appeared in various Marvel comic books: