After the events at the Raft, Akira and Hikaru are taken aboard the Helicarrier while the other three are sent safely home. There, Nick Fury and a tiny hologram Iron Man (from inside the red DISK) reveal that because the biocode installer was damaged when it installed a biocode in the kids, the kids have a Limited Biocode, which only allows the released heroes to be outside the DISK for a few minutes and also requires hours to recharge. A man by the name of Senator Robert enters with incriminating photos of Fury, Tim, and Loki, leading to Fury's arrest and the ...

Hikaru accepts Hawkeye's offer and parachutes down to a building near the scuffle with Diamondback against direct orders from Robert and Hill. With a little help from Akira, Hawkeye manages to leave Diamondback distracted long enough for Hikaru to stop the disguised Riley from stealing more DISKs from within a bank. Unfortunately, Riley sends out King Cobra to send Hikaru flying. After being caught by Spider-Man and handed Thor's DISK, Hikaru releases Thor, who interrupts King Cobra's offer to finish the kids off in exchange for permanent freedom with a hammer toss. Diamondback throws a fragment bomb diamond to ensnare everyone, but Thor uses a whirlwind/lightning combination to destroy the bomb and force Diamondback to surrender. Riley is forced to withdraw King Cobra and escape with Tim and M.O.D.O.K., as Hikaru and Thor introduce each other formally. Later, Pepper and Iron Man give Akira and Hikaru a place to stay in New York while the crisis continues.

Spider-Man tries to convince Chris to help out with the DISK effort, but Chris refuses due to sheer lack of interest. Spider-Man begrudgingly admits defeat in the manner, considering how Ed refused due to overwhelming cowardice and Jessica due to being preoccupied with luxuries. After tossing Captain America's DISK to Chris regardless, Spider-Man is attacked by Joel and Abomination.

Captain America begins to face Hulk, still on a rampage from Diablo's alchemic control, and starts by playing defense with his vibranium shield to gauge the situation. While Hulk is distracted, Akira and Hikaru recall Iron Man and Thor, who desperately needed time to recover. After forcing Hulk to tire himself out, Captain America goes from playing defense to outwitting Hulk to forcing him into a test of endurance, which Hulk loses. Akira secures Hulk in a new DISK, freeing him from his control. Meanwhile, Jessica and Ed escape their room on the frigate to where Spider-Man is being kept, and are found by Tim.

Reunited at last on the frigate, the Avengers face off against Loki's cohorts while a harshly weakened Spider-Man struggles to survive below deck. Everything seems to be going well until Loki arrives disguised as Hikaru, tricking Thor into taking a Cane Blast point blank. Seeing the need to retreat, Loki orders Abomination to sink the Frigate, and then retreat. Jessica and Ed manage to capture a defeated Whirlwind, Diablo, and King Cobra while Captain America, Hulk, and Wasp try to find Spider-Man before it's too late. Spider-Man, dreaming of his "reported demise" and "triumphant return" to New York, wakes up to find the Avengers carrying him out of the ship. Later, while the team is having a celebration, Senator Robert closes in on Stark's penthouse in New York with a new warrant for either registration or arrest.

Hikaru and Pepper secure the DISKs that the team has obtained so far while everyone else is at their own activity. Jessica spends time trying on new clothes at a fashion shop, Ed spends time showing off his knowledge at a superhero memorabilia store, and Chris spends time sampling Japanese cuisine at a restaurant.

With the D-System fully operational, everyone heads out to a desert to locate a hidden DISK. Ed packs his bag too heavily, and ends up slowing everyone down. Chris offers to help him out, but expresses his disgust for Ed's weakness. They run into Joel and Absorbing Man, who accidentally reveal that Nozomu is in fact alive and well. Joel is summoned by a phone call from his agent, so he leaves Absorbing Man to take care of the Avengers. He completely withstands attacks from Wasp and Thor, but is eventually defeated and captured due to his arrogance.

While Wasp, Captain America, and Thor keep Tim and a couple of his Tech villains busy, Akira and Ed attempt to get their hands on a new DISK from a dangerous location in a construction site. Ed D-Smashes Hulk by mistake, shaking the structure and accidentally knocking the DISK down.

Hikaru, Chris, Ed, and Jessica play a hero combat video game using their partner heroes as characters, and Jessica becomes very tired of Hikaru winning all the time. Insisting that such a perfect person like Hikaru must have some weakness, Jessica demands one more round on the game, but the power goes out before they get the chance. Akira had been playing with a mechanical arm and had accidentally cut the power temporarily, but since Hikaru didn't know that he used all the furniture he could to break down the doors on the way to where Akira is located.

When the next DISK appears to be located around Jessica's house in France, she offers the team a place to stay while they are going after it. However, when Akira thanks her, she states that it was done solely out of noblesse oblige and has nothing to do with friendship whatsoever.

After seeing how managing schoolwork while staying around the base was proving difficult for everyone, Iron Man and Pepper decide to take everyone to Techno Isle Tokyo, a miniature city outfitted with the latest surveillance and security technology by Stark International.

While Wolverine and Sabretooth are staring each other down (with Iron Man reluctantly standing back), they are interrupted by three Destroyers being D-Smashed onto the scene. Seeing as how he wouldn't allow anyone to interrupt his rampage, Sabretooth obliterates one of the Destroyers and sets off after Ōkuma and Riley. Thor advises the Avengers and Wolverine to go all out, since the Destroyers are lifeless husks. Sabretooth threatens Riley since she intervened, but Ōkuma and Manino D-Secure him, noticing that the DISK changed shape due to his mutant nature. Back on the battle scene, the Avengers take down one Destroyer while Wolverine takes down the other with some help from his healing factor. A safe distance away, Iron Man apologizes for what happened to Cyclops and offers Wolverine to join the DISK-securing effort.

Despite Noriko still being in shock, Wolverine tries to convince her to come to the Xavier Institute. She refuses, still in denial about being a mutant to begin with. Begging Hikaru to keep it a secret, she runs off. Later, the Avengers fight the Wrecking Crew while trying to get a DISK. The battle seems to be going in the favor of the Avengers, but Hikaru is still distracted by thoughts of Noriko, which nearly gets Thor beaten by Thunderball. After Iron Man swears revenge against the Wrecker for his humiliation on the Raft, the Wrecker creates an earth tremor with his crowbar and sends construction equipment falling down.

Wolverine tries to comfort Noriko, telling her that at the Xavier Institute she will have friends who have been through exactly the same thing and can help her learn to deal with being a mutant. He also tells her that trust is a big part of being a mutant, and how she really does need people she can rely on. Later that night, Hikaru apologizes to Noriko about the whole deal over coffee, stating how it doesn't matter to him what she is, and Noriko accepts the apology whole-heartedly.

With Wolverine paralyzed by Predator X and Cyclops overwhelmed by Baron Zemo, the battle does not bode well. Despite Wolverine's adamantium skeleton being too difficult to pick up, Hikaru attempts to carry Wolverine off to safety. Hikaru's determination to save Noriko and prove useful keeps him going, but the tide of the battle turns hopeless once Cyclops runs out of time and automatically returns to his DISK.

In Jotunheim, Loki has one final gloating moment with the helpless Avengers. Iron Man and Thor express how not capturing Captain America that moment was extremely foolish, but Loki ignores them and proceeds with his plan anyway. Loki reveals a technological chamber containing all the DISKs in his possession, and declares that he plans to use the device to absorb all the powers of heroes and villains alike into his own being, hence becoming all-powerful.

With the Avengers assembled for the final battle against Loki, the Celebrity Five flee and Nozomu steps back with the kids. After Iron Man and the Akatsukis give each other their thanks, Thor attempts to have Loki be ashamed of stealing the powers of others.

Akira and the other children are still recovering from the affects of Synchronizing their Biocodes with the Avengers. Crossbones frees Loki's former henchmen, who are on their way to prison, in order to gain their Biocodes. A possible trip to the hot springs with Sunfire is interrupted by the discovery that Mystique has stolen the Avengers' remaining villain DISKS, disguised as Pepper, in exchange for being freed from her DISK by Red Skull. Sunfire tracks her and interrupts Crossbones as he is about to shoot Mystique. He attacks the Red Skull, but is badly injured by him. Red Skull has gained a full Biocode installation for himself and Crossbones from Loki's former henchmen, using the red Dimension Sphere, which has the power to make miracles a reality. He D-Smashes the villains to stalemate the Avengers and escape.

An escape pod containing Rocket Raccoon and Groot is stopped by Iron Man and Hulk from crashing in Techno Isle, Tokyo. The pod also contains the Kree Mact, a powerful blue energy device stolen from Ronan by the Guardians of the Galaxy. Iron Man reluctantly agrees to board the Helicarrier in order to study it. Eventually Rocket and Groot revive, just as the other members of the Guardians arrive to take back the device and their comrades. The Avengers fight with the Guardians, but settle their differences just before a vortex opens and a large creature emerges.

The large creature is Fin Fang Foom and he toasts the Helicarrier with his flame. A cobbled together beam weapon is built by Iron Man and Rocket Raccoon, using the Kree Mact as its power source. The beam strikes Fin Fang Foom and knocks him out. Hikaru D-Secures him. Ronan soon appears, angry that the Kree Mact was used thus and wanting it returned. Iron Man stalls for time, asking for an hour to vote. Ronan drains power from the Helicarrier, causing it to crash land in the sea, but agrees to give them an hour. The Heroes attack separately, but are swiftly defeated by Ronan's ability to absorb and control energy. They regroup and attack as a team, with help from Hawkeye, draining Ronan briefly. Defeated, he teleports away. Captain America offers for the Guardians to join the Avengers, but they decide not to. They leave the Kree Mact with the Avengers, to Iron Man's delight, and take two smaller decoys with them.

A partial recap episode. Tony and Akira reminisce about their adventures together insofar. Meanwhile, M.O.D.O.K. hacks Tony's data base and steals the data they have collected throughout the series.

While out getting chimichangas and money, Deadpool encounters King Cobra at a "villain joint", defeats him and takes Iron Fist's DISK. Later, he shows up at Avengers headquarters, offering the DISK in return for becoming the leader of the Avengers. King Cobra shows up with Cottonmouth and Diamondback of the Serpent Society, wanting the DISK back. Deadpool (with the backing of the Avengers) easily defeats and the kids D-Secure them. The team refuses his request and he leaves, replacing the captured DISKs with joke fakes. Later, Tiger Shark shows up, wanting him to turn on the Avengers. He is refused and is about to attack Deadpool, when the Avengers show up. They had planted a tracker on his uniform when he was in the shower. Tiger Shark is about to attack them all, despite their bluff of using Iron Man's new armor, when Red Skull D-Secures him, having warned him to stay away from the Avengers.

Hawkeye and Falcon lead a mission to save a researcher but when Hawkeye can't make it out he tells Falcon to go without him telling him to take care of the kids at all costs. The Avengers get a message from Red Skull saying that he plans to destroy the world and in the world that is recreated there will be a new law in which good never triumphs. With five bases and five avengers the kids split up. Akira, Iron Man, and Falcon go to the first hideout and take on Whiplash and Crimson Dynamo. Akira senses that Falcon is troubled due to Hawkeye's absence and doesn't allow Falcon to take any unnecessary risks saying that Hawkeye wanted Falcon to be safe just as much as the kids. Akira and Iron Man then take on M.O.D.O.K. who controls tech disks and sends them on Iron Man. Falcon is able to save Iron Man but gets badly injured. Iron Man then defeats M.O.D.O.K. with his new invention. Due to Falcon's bad wounds, Akira D-Secures him and makes Falcon his second hero.

With the threat of Red Skull's world destruction plan, Jessica and Wasp go to Wakanda to find the second base. Jessica meets Black Panther, who has been overthrown by Tiger Shark who oppresses the people of Wakanda and forces them to be slaves. Jessica and Black Panther come up with a plan to free the slaves and stop the threat at the same time. At first the plan goes sound, but Jessica gets captured by King Cobra and the Serpent Society, leaving Black Panther to fend for himself. Black Panther frees Jessica but then gets D-Secured by Tiger Shark. Jessica D-Smashes Wasp who with Iron Man's invention saves Wakanda. Jessica then takes the D-Secured Black Panther as her second hero.

Black Widow/Natasha Romanoff arrives outside Deadpool's apartment building. In his apartment, Deadpool is trying to sell Iron Fist's DISK to Taskmaster, but the other is uninterested in the offer and hangs up on him. Black Widow then calls on Deadpool at his apartment in order to hire him for a mission. Deadpool accepts the payment - after proposing to her. Meanwhile Chris, Captain America, and their S.H.I.E.L.D. escort arrive at Baron Zemo's base, where the villain is to launch the next part of the Red Skull's plan. The group enters through a supposedly unguarded tunnel, but are surprise attacked by the Green Goblin and several HYDRA agents.