On the eve of the Super Hero Squad disbanding forever, Captain Marvel vanishes on his way to a peace mission between the Kree Empire & the Skrulls.
The Super Hero Squad are called in & an attempt to negotiate a peace.

Meanwhile, Thanos begins his quest to obtain all the Stones for the Infinity Gauntlet & back on Earth Dr. Doom attempts a prison escape with the help of Thunderball & Wrecker.

The Super Hero Squad sit imprisoned by the Skrulls until Falcon reveals the presence of The Scarlett Witch who has stowawayed on the Helicarrier.

With Thanos using the Soul Stone to manipulate the Skrulls & Kree into war, Scarlett Witch must rescue the Squad and stop the fighting.

Zeus challenges Odin in a favorite son contest pitting Hercules against Thor.
However things don't go as planned after Loki steps in.

The Mayor enlists the Invisible Woman to film the contest so he can air it on TV as a pay-per-view event to raise money for the city.

When Thanos acquires the Time Stone, he tests it out of Falcon and the Scarlet Witch.

Scarlett Witch stops him but as a result, his power sends her back to World War 2 Earth where she teams up with a past version of Captain America and his team to stop The Red Skull from launching a giant rocket that could turn the tide in the war.

Doctor Doom, MODOK & Abomination hatch a plan to escape prison by using a giant balloon to distract the Super Hero Squad while they dig their way to freedom.

However the plan goes south when Captain America & Ms. Marvel step in to stop them but Doom calls in backup with his friends, Molecule Man & Volcana.

A being called Grandmaster with the encouragement of Thanos transports Iron Man, Hulk & Scarlett Witch to another dimension & forcible challenges them fight The Squadron Supreme.

Meanwhile, Reptil complains about Scarlet Witch becoming a full time Squaddie over him while he, Wolverine & Thor search for their missing teammates.

When Galactus threatens the Skrull throne world, Princess Anelle enlists The Super Hero Squad to help save her world.

Ronan the Accuser attempts to find The Silver Surfer in attempt to help stop Galactus but quickly realizes the power of the Infinity Sword has corrupted him.

Thanos finds the Space Stone but after it's taken by his sister Nebula. She attempts to use the Squad's jump station to escape but a malfunction sends her and the Hovercarrier to the Negative Zone.

Thanos controls the sleepwalking Hulk by using the Mind Stone which draws the attention of The Thing who decides to take matters into his own hands in stopping him.

When Iron Man, Thor & Wolverine attempt to break up their fight, they are sidetracked by Nightmare.

The Sorceress casts a spell on Odin making him fall in love with her forcing him to abdicate the throne of Asgard.
When Thor hears of this, he returns to Asgard and assumes the throne.

Meanwhile, Quicksilver & Magneto, upon hearing The Scarlett Witch in on the Helicarrior, attempt to rescue her thinking she's being held prisoner.

Thanos attempts to obtain the Power Stone from the Nova Corps.
Before he can be captured, Nova calls the Super Hero Squad for help.
Iron Man enlists Hercules and She-Hulk for the journey.

When hundreds of Wolverines start to appear around the city, Reptil, Firestar & the original Wolverine track down the source of the copies.

Doctor Doom returns to his native homeland only to discover that his beloved Castle Von Doom has been transformed into a hotel by his mother.

Coco Von Doom lures the Super Hero Squad to her spa with the intentions of destroying them.

When Thanos acquires the final Infinity Stone, the Super Hero Squad faces a final confrontation with the help of a friend.

However things don't go as planned when the Silver Surfer betrays his former comrades.

The Dark Surfer sends Thor to a space station in the midst of a battle with The Stranger.

Thor meets the station's janitor, Beta Ray Bill, whom he helps achieve his true potential.

The Dark Surfer sends Falcon & HERBIE to a world ruled by an alternate version of the Scarlet Witch known as the Scarlet Empress.

They team up with an elderly Magneto to free the imprisoned world's greatest hero, The Man, so they can stop the Scarlett Empress.

Iron Man lands in a village that's plagued with mummies, werewolves, vampires and a large swamp creature.

Things get worse when the dimensional rift drains his suit of its reserve powers.

After being thrown into another dimension by the Dark Surfer, Wolverine befriends Moon Boy and his Devil Dinosaur.
Wolverine must help them from a gigantic robot named High Evolutionary.

Meanwhile, The Mayor hijacks a Squaddie vehicle to confront the Dark Surfer on his own which only annoys the Surfer which causes him to send Earth hurtling into deep space.

Hulk lands on a planet Sakaar and is forced to enter gladiatorial combat by the Red King.

Meanwhile, Reptil with the help of Firestar & the Human Torch attempt to keep the Earth warm until they can devise a plan to return it to its orbit.

Scarlet Witch lands in the year 1602 where she must help the newly founded Super Hero Town face Captain Doom & his pirates while defending herself from charges of witchcraft.

Meanwhile Dr. Strange helps the rest of the Squad find the missing members.

In a last ditch effort to save their fellow Squad members, Ms Marvel & Mr. Fantastic join Captain America in the Savage Land to attempt a daring experiment but things go awry when Cap is kidnapped by Baron Strucker and Hydra who are attempting to flee Earth.

Before the team heads out to confront Dark Surfer, The Super Hero Squad is visited by Impossible Man.

He attempts to impress his estranged wife by taking on the Dark Surfer himself.

Iron Man invents a time traveling device in order to return to the moment right before Silver Surfer takes the Infinity Gauntlet from Thanos turning him into the Dark Surfer.

However, Dark Surfer finds out Iron Man's plans and destroys the device and as a going away present, transforms Iron Man, Falcon & Scarlet Witch into toddlers forcing Wolverine & Hulk to babysit while Thor, Ms. Marvel & HERBIE search for a way to transform them back.

Captain Marvel joins the team in their fight with Dark Surfer but things go wrong when Ms. Marvel, Thor and Iron Man end up in the Soul Stone with Thanos and Warlock.

Thanks to the knowledge obtained from Warlock inside the Soul Stone, the teams devises a plan to defeat Dark Surfer.

Meanwhile, Doctor Doom devises his own plan to defeat Dark Surfer only to obtain the Infinity Gauntlet for himself.

Once the Dark Surfer is defeated and the Infinity Gauntlet destroyed, things have not gone back to normal until the Super Hero Squad realizes the Infinity Sword is still somewhere in the cosmos.

With Ronan the Accuser's help, the Squad locates the Cosmic Infinity Pool which leads to a surprise confrontation with Doom.