The Squadron Supreme are the only superheroes on their Earth in a universe parallel to our own. After being mind-controlled by an alien called the Overmind and ruining their Earth, they freed themselves but found that their people hated them for what they had done. Partially responsible for the chaos enveloping their world, they chose to take control of the planet to solve its problems. As such they took active responsibility for more than just fighting crime and supervillains and took on poverty and hunger, the environment and public health. The original team comprised Hyperion, Nighthawk, Doctor Spectrum, Amphibian, Power Princess, Whizzer and Skrullian Skymaster.
Squadron Supreme were created by Roy Thomas and John Buscema and first appeared in The Avengers #85. The members of the team were created to deliberately mirror major characters of the Justice League: Superman, Batman, Green Lantern, Aquaman, Wonder Woman, Flash and Martian Manhunter.
This direct copying was not some spontaneous idea of Marvel's but was rather a part of efforts on both sides in the 60's to create an unofficial crossover of sorts. In fact, some of these replica characters had appeared earlier in The Avengers #69, but in this case as villains as part of the Squadron Sinister (Doctor Spectrum, Hyperion, Whizzer and Nighthawk). They were later retconned to be an artificially created team of copies of the heroic Squadron Supreme, made by Grandmaster (who supposedly knew about the alternate universe of Earth-712 and its Squadron).
Simultaneously, DC's own effort in this vein was the appearance of Champions of Angor in the same month, in Justice League of America #87.
After their initial encounters with the Avengers and Defenders, the Squadron Supreme were given their own 12 issue limited series, written by Mark Gruenwald. Here, Gruenwald took the opportunity to explore and challenge superhero storytelling conventions free from Marvel continuity and write a story where super heroes took over and actively ruled a planet. By this time, the roster had expanded to include yet more DC analogous characters: Arcanna Jones (mirroring Zatanna), Golden Archer (Green Arrow), Blue Eagle (Hawkman), Lady Lark (Black Canary), Nuke (Firestorm) and Tom Thumb (Atom).
Other members join during the Squadron Supreme series: Ape-X, Dr Decibel, Foxfire, Lamprey, Quagmire, Shape, Haywire, Inertia, Moonglow (Melissa Hanover), Redstone, Thermite and a new Nighthawk (Kyle Richmond's son Neal).
Major Story Arcs
Against the Avengers
The first appearance of the Squadron Supreme sees them come into conflict with the Avengers from Earth-616, when Scarlet Witch, Quicksilver, Hawkeye (as Goliath) and Vision are transported to Earth-712. Although the teams fight each other at first, they eventually join forces to defeat Brain-Child's plans to destroy the Squadron's world.
The Avengers met the Squadron again later while investigating the operations of the Roxxon Corporation. Roxxon's Hugh Jones, under the control of the Serpent Crown, summons the Squadron who defeat the Avengers and put them in prison. The leader's of the Squadron's world themselves are under the Serpent Crown's influence. When both teams are sent back to Earth-712, the Avengers help the Squadron to free themselves from its manipulation and defeat their foes.
Defenders and the Overmind
Perhaps the most crucial episode in the Squadron's history came when they again fell under mind-control, this time by the Overmind. The Overmind, under the direction of Null the Living Darkness forced the Squadron Supreme to take over their own planet and subjugate its people, helped by the fact that Nighthawk (Kyle Richmond) was the President of the US at the time. The Defenders of Earth 616 came to the rescue this time, helping the Squadron to rebel against the Overmind, but sadly leaving the planet in a chaotic, ruined state.
The Utopia Program
Following the defeat of the Overmind, the Squadron made plans for the future of their world. Wanting to restore order, Hyperion has the idea that since the Squadron members have great knowledge and power, they themselves could solve all their society's problems by directly ruling over them, in spite of the people's mistrust and hatred. After a vote they decide to implement the Utopia Program, a scheme in which they would proactively work to help the world instead of always reacting to crises, starting by taking over the US government for a year. Believing that this would only set up a new form of dictatorship, and that humanity itself must bring about its own 'Utopia', Nighthawk resigns rather than assist the team in their project.
Nighthawk, after seeking but failing to get the help of the 616 Avengers, joins forces with the Squadron Supreme's former enemy Master Menace and assembles a new team called the Redeemers to free the world. Nighthawk and his rebels fight the Squadron, leading to his death in the final battle. The shock of this tragedy makes the Squadron realize they were in the wrong and they start to undo their Utopia Program.
The Nth Man
In the ensuing days after the Squadron Supreme's battle, a being of unlimited power called the Nth Man appears, planning to destroy the entire universe. The team along with Professor Imam and Master Menace travel by space shuttle to confront this force in its location behind the Sun. A desperate struggle leads to Arcanna offering her baby son Benjamin to switch places with the Nth Man (revealed to be Dr Thomas Lightner), defeating him and reversing all the damage he had done.
Trapped on Earth 616
Following the defeat of the Nth Man, Master Menace sent the Squadron Supreme into exile outside their dimension, resulting in them ending up in Earth 616. The Overmind woke up upon their arrival in our Universe and brought them under its control again, using them to attack the Stranger on his Laboratory World. Power Princess broke free from Overmind's domination and together with the Stranger they defeat the Overmind. Having met Quasar, the team chose to hide out at Project: Pegasus.
Next, Imus Champion used the Corruptor to mentally influence the team yet again, making the Squadron believe that the Avengers were still dead after the Onslaught Saga and making the two teams fight. Champion used the situation to defeat both sets of heroes and was only beaten by the timely intervention of Giant Man.
Global Directorate and The Exiles
Using equipment called the 'Nth Projector' found in Imus Champion's collection, Iron Man helped the Squadron Supreme to return to Earth-712. On arrival they discovered that their world has been taken over, this time by a corporate dictatorship called the Global Directorate who are using a behavior-modified Master Menace and his technological genius to rule the people. The team were considered enemies of the state.
Mysterium (formerly the Nth Man/Dr. Thomas Lightner who had tried to destroy the universe) approaches the team and gets them to regroup with other original members to fight the Directorate. A new Nighthawk, Kyle Richmond's son Neal, joins as well. The team take up residence on Utopia Isle from where they can fight the forces of their corporate enemies.
Somehow, Proteus (an escapee from the House of M) arrives on Earth-712. He helps the team fight off the Blue Eagles - the Global Directorate's shock troops - and weasels his way into the Squadron's good books in an attempt to get them on his side when the Exiles (the interdimensional superteam who are on his trail) arrive. The Exiles show up and are attacked and put on trial by the Squadron, while Proteus escapes. With the help of Heather Hudson, the Exiles reveal to the Squadron that somehow once again they have been duped. The Squadron Supreme and the Exiles team up to depose their fraudulent government, and then Power Princess joins the Exiles to go after Proteus, becoming a member of their team until his capture.
The Squadron Supreme does not exist in the main Marvel Universe (Earth-616). The original Squadron exists in Earth-712 and another exists in Earth-31916 ("Supreme Power").
The Squadron Sinister, a team which first appeared as an enemy of the Avengers in Avengers #69 (and so predating the first appearance of the Squadron Supreme) is made up of exact copies of some of the Squadron Supreme, those being: Doctor Spectrum, Hyperion, Whizzer and Nighthawk. In the Squadron Supreme series, this similarity is explained as being due to the villain Grandmaster creating a team of villains modeled after members of the already existing (in his world) Squadron Supreme.
While Earth-712's Squadron was trapped on Earth, a deranged scientist named Mortimer Dauoi convinced the Squadron that knowing each member's individual DNA codes would make great leaps in science and had Doctor Spectrum make hard-light constructs of each member's individual helixes. After the Squadron returned to Earth-712, Mortimer grafted their DNA onto medical cadavers.
In order to complete his experiment, Mortimer required a powerful energy source to reanimate his test subjects and found that source in the form of Zeta Rays, which were made up of negatively charged energy thrown off by agitated atoms. Because continual exposure to Cosmic Rays kill normal brain cells, Mortimer correctly theorized that Zeta Rays would have the opposite effect on dead brain matter.
It worked and then everything went straight to Hell. The cadavers, which had become undead doppelgangers of The Squadron Supreme thanks to exposure from the Zeta Rays, awoke with a ravenous hunger for human flesh. One possible reason for this unimaginably terrifying turn of events was traced to the refracting nature of a prism, which more than likely made Spectrum's DNA constructs unstable.
When Project: P.E.G.A.S.U.S. went dark and was sealed shut from the inside Jill Harper and her Guardsman Alpha Team, along with Battlestar, were sent to investigate and were spotted by a roaming Whizzer, who decided to keep quiet and watch from the shadows rather than straight up attack Jill's crew. As Jill and her crew continued down the corridors of Project: P.E.G.A.S.U.S., they discovered a large amount of blood and brain matter splattered all over the floors and walls.
Their presence drew the attention of "Tom Thumb", the monster responsible for all the carnage, who made a move against his new prey and ended up being shot in the head by Hoss, one of Jill's subordinates. Doc, another of Jill's subordinates, determined that Thumb had been dead long before Hoss blew his brains out.
Jill and the others moved to a nearby room to find a group of survivors huddled around a computer terminal holding blueprints and a case containing a possible solution to the current crisis. Though some of the scientists were relieved to see Jill and her crew, Jill had failed to realize that her actions had allowed "Nighthawk" to slip in unnoticed, until he took down one of the scientists. Despite their attempts to stop him, Nighthawk not only managed to infect almost all of the scientists but got his hands on the blueprints.
Just as Jill was about to shoot him, "Hyperion" and the other members of the undead Squadron Supreme appeared to join in on the feast. The events that followed their arrival resulted in a mass slaughter that took the lives of Jill's teammates Two-Ton and Doc and forced Jill into retreating, but not before managing to temporarily disable Hyperion with some Argonite, forcing the other Squadron members to focus all their attention on keeping Hyperion healthy.
While Jill and the others were attempting unravel a new mystery that Mortimer had left behind, Hyperion and The Zombie Squadron made their way to a magma pool that supposedly lead to the Earth's core. With Hyperion being the only one able to survive a trip straight through the core, he leaped into the magma pool and managed to reach the outside world.