Season 2 episodes of the Heroes Alliance.
- The Man of Steel!(PLOT: With Kamen Rider Den-O helping them, the Heroes Alliance are able to stop Brainiac from altering Superman's timeline, as a baby. While trying to expose Lex Luthor, Superman battles his advance.)Introducing characters: Superman, Kamen Rider Den-O, Lex Luthor, Brainiac
- The Coming of Galactus!(PLOT: The Green Hornet and the Heroes Alliance defeat the Riddler while trying to escape his deadly game show. The Heroes Alliance team up with the Fantastic Four to battle Galactus and his herald: the Silver Surfer!)Introducing characters: Green Hornet, Mr. Fantastic, Thing, Human Torch, Invisible Woman, Galactus, Silver Surfer, El Chapulin Colorado, Proto Man,
- Flaws of the Flamingo!(PLOT: The Heroes Alliance help Leonardo with his ninja training. The Heroes Alliance help Captain Flamingo rescue his girlfriend and family members from Satanai and Amobea, a villain seeking revenge on Captain Flamingo.)Introducing characters: Leonardo, Satanai, Birdbrain, and Amobea.
- The Super Soldier Strikes!(PLOT: The Heroes Alliance and Aquaman team up to stop the Ocean King from overthrowing Aquaman to become king of Atlantis. The Heroes Alliance discover a frozen Captain America in the Arctic, and thaw him out so they can defeat the Red Skull, who is thawed out by Zemo.)Introducing characters: Aquaman, Ocean King, Captain America, Red Skull, Baron Wolfgang Von Strucker, Viper, Grim Reaper, Doughboy, Nadya, Jean Pierre Polnareff
- Articuno and Its Arts!(PLOT: Rambo teams up with the Heroes Alliance to take out al-Qaeda terrorists from detaining a deadly nuclear bomb. Ash, Pikachu, Misty, Togepi, Brock, and the Heroes Alliance protect an ailing Articuno from Team Rocket and Rita Repulsa.)Introducing characters: Rambo, Misty, Togepi, Brock
- Merge, Metal Men!(PLOT: With the Heroes Alliance aiding them, Inspector Gadget escapes a death trap. The Heroes Alliance help the Metal Men rescue their creator from the Gas Gang.)Introducing characters: Inspector Gadget, Penny, Brain, Gold, Lead, Iron, Mercury, Platinum, Tin, Oxygen, Hydrogen, Chloroform, Cardon Dioxide, Carbon Monoxide
- The Power of Green!(PLOT: The Heroes Alliance rescue the Hulk before the Leader absorbs his powers. The Green Lantern Corps enlist the aid of the Heroes Alliance to defeat Despero.)Introducing characters: Hulk, Leader, Abomination, Tigershark, Guy Gardner, Sinestro, Yumi, Eddy, Dorgo, Despero
- An Attack on Asgard!(PLOT: The Heroes Alliance help Kamen Riders Ichigo and Nigo stop Black Shogun and his army from releasing a deadly nerve gas. The Heroes Alliance head to Asgard to help Thor battle Loki, while the Red Ranger's teammates hold off the Wrecking Crew.)Introducing characters: Black Shogun, Thor, Loki, Enchantress, Executioner, Absorbing Man, Thunderball, Wrecker, Bulldozer, Piledriver
- All Hail H.Y.D.R.A.!(PLOT: Viper sends down the Serpent Society to destroy Josh Holo and the Heroes Alliance. Captain America and Iron Man recruit the Heroes Alliance to take down H.Y.D.R.A., with Baron Zemo and Arnim Zola joining them.)Introducing characters: members of the Serpent Society, Birdy the Mighty
- The Deaging Spider!(PLOT: Mark of the G-Force help the Heroes Alliance detain Birdbrain before he unleashes a nuclear egg. Dr. Drakken rounds up Spider-Man's enemies to build a doomsday device, and also zaps a deaging ray on Spider-Man.)Introducing characters: Mark, Birdbrain, Kim Possible, Ron Stoppable, Rufus, Dr. Drakken, Shego, Sandman, Rhino, Mysterio, Fly, Mystique Sonya, Grimjack, Odu-Bathax, Jumpy Ghostface, Mighty Ray, Lin Chung, Feedback
- Welcome to the Jungle!(PLOT: G.I. Joe and the Heroes Alliance to battle Cobra. The Black Panther asks for the Heroes Alliance's help when Man-Ape kills his father and rules his village with corruption.)Introducing characters: Duke, Duke's teammates, Cobra Commander, Destro, members of Cobra, Black Panther, Ant-Man, Wasp, Man-Ape, Klaw(later becomes the Sound), Marsupilami
- Doom By the Decepticons! Part 1(PLOT: Plastic Man and the Heroes Alliance stop Kite Man from activating a bomb disguised as a giant kite. Megatron unleashes a deadly force against the Heroes Alliance.) Introducing characters: Plastic Man, Kite Man
- The Might of Megatron! Part 2(PLOT: Megatron kidnaps Red Ranger, Greymon, and Spider-Man in order to operate a deadly artifact for world domination. So, Optimus Prime turns to his old teammates--the Autobots!)Introducing characters: none