Marvel Super Heroes is based on a storyline from the comics. In 1990, Marvel released The Thanos Quest, a two issue series which shows how Thanos gets the infinity gems.
In 1991, Marvel released The Infinity Gauntlet, a six issue series. The series stars Thanos, who has attained god like powers after collecting all of the infinity gems together, and putting them into the infinity gauntlet.
Thanos attempts to win the heart of Death herself, but no matter what he does, he cannot get her to show any affection for him. Under the guidance of Mephisto, Thanos uses his new powers to try and impress his love, and destroys half of the life in the entire universe. This devastates the Earth, and many super heroes -such as the Fantastic Four, Hawkeye and Daredevil -are simply removed from existence in an instant. This still doesn't impress Death and in a fit of rage, Thanos releases a huge wave of destruction across the universe. This further devastates Earth and some countries, such as Japan, are completely destroyed. This is referenced in the game in Captain America's stage, which shows a destroyed New York.
Adam Warlock gathers together a team of heroes to fight against Thanos. His team consists of Captain America , Cloak, Cyclops, Dr. Doom, Dr. Strange, Drax, Firelord, Hulk, Iron Man,
Nova, Quasar, Scarlet Witch, She-Hulk, Silver Surfer, Spider-Man, Sub-Mariner, Thor, Vision and Wolverine. Most of these heroes are simply sent on a suicidal mission, but they are not told this. Adam uses them as a distraction whilst he and Silver Surfer wait far away from the battle. Adam tries to get Silver Surfer to enter the battle at a precise moment, so he can steal the infinity gauntlet from Thanos.
Magneto, Juggernaut, Blackheart and Shuma-Gorath do not appear in the comics at all. Psylocke does appear in a single panel of the first issue. I guess the reason she was put in the game was due to the unspoken rule that Street Fighter II created: every fighting game has to have at least 1 female character in it.
Psylocke was fairly popular and Capcom could just use her sprite from Children of the Atom, so I guess that was why she was put in the game over the likes of She-Hulk or Scarlet Witch.
To try and impress Death, Thanos creates a shrine for her. It looks like this:
And here is the video game version of it, ripped by Professor InvinciBeef:
The video game version features Mephisto (the man in red), Death (woman in purple) and several heroes turned to stone- there being, from left to right, Drax, Nova, Thor, She-Hulk and Scarlet Witch. If you beat the game with one of the good side characters, these heroes are released and turned back to normal.
When Thanos uses his mind gem super, the background changes to a picture of him with the Infinity Gauntlet. The picture is taken from the first issue.
The cover to issue four features Thanos taunting. His words can be seen in the game as one of Thanos' win quotes.
Also in issue four, Thanos kills Quasar. The words Thanos tells Quasar as he kills him were slightly changed and used as a win quote in the game.
The ending in the game, where Thanos takes more power, is based on a scene in the fifth issue where Thanos defeats Eternity and takes his place as the grand God. However in the comics this proves to be his downfall as he no longer has control over his physical body, meaning he no longer has control over the powers of the Infinity Gauntlet. This lets someone else take it and reverse everything he has done with it.
In the comics, Thanos attempts to destroy himself by exploding a nuclear device, but Thor knocks him away and a huge explosion takes place. Thanos isn't dead, and has retreated to a small planet to live a simple life. However Adam Warlock, who has now taken possession of the infinity gauntlet, knows he has survived and visits him. He finds Thanos' old costume being used as a scare-crow and not far away, Thanos himself appears. In the game, you can see the scare-crow and farmer Thanos if you pick the second ending where he gives up the power he has.
Juggernaut's ending features Adam Warlock in a pose that looks very similar to his appearance on the front cover of Warlock and the Infinity Watch #1:
Whilst the game only covered the Infinity Gauntlet storyline, the comics would go onto have two sequels: Infinity War and Infinity Crusade.