Seeing Heroman's power before his own eyes, Joey wasn't able to hide his happiness or bewilderment. He worries about what he should do with this power and what Heroman really is. Meanwhile, the mysterious life forms called "The Skrugg" have begun their Earth invasion. When Joey hears of it, he runs to tell Prof. Denton who was broadcasting to them of the imminent danger. However, the Skrugg appear there with weapons in hand! And Lina encounters them as well!?

The giant saucer that appeared in the skies of Center City begins sending tons of Skrugg down to the ground. Even with the military in wait, they were no match for the onslaught, and the people could do nothing but escape. After Joey stands in shock watching the neighborhoods being destroyed, he and Psy head to Joey's grandmother's house. However, the Skrugg show up and get in their way. Joey steels his determination, activates Heroman, and stands up, ready to face the enemy himself.

Will thinks that he should be the hero, and drags Nick along with him to infiltrate the enemy's base and steal some of their weapons. At the same time Joey, having successfully dropped off his grandmother at the shelter, heads toward Professor Denton's place to get more information. On the other hand, Kogorr starts attacking with a giant sphere. And what's more, it's started rolling straight toward the shelter where Grandma and Lina are! Joey and Heroman head out to face it and stop its advance somehow.

Against the rolling sphere that continues to destroy the city, Joey and the others could do nothing but barely hold its progress. Joey is determined to not leave the Skrugg alone, and leaps into the fray again even without a plan, while Prof. Denton gives a guitar weapon to Psy that he created using the Skrugg's weapon. Joey and Psy head into the city with the weapon in hand, and they come up with a new plan to go up against the huge number of Skrugg. But before them a new threat comes calling...

Joey's group is forced to retreat from the new enemies that suddenly appear in front of them. Meanwhile, Prof. Denton has analyzed the Skrugg and determined that the five spheres are heading toward different important world cities. One of them is the White House itself. At first thought to just be rolling spheres, it seems the Skrugg studied humanity well on how exactly to destroy the entire world. Realizing this, everyone is shocked and itching to do something about it, and as the time limit approaches, Joey and his friends become determined to head toward the enemy's base.

Faced with the extinction of the human race, the President is coming closer to deciding to use nuclear weapons. But before him appears the mad scientist, " Dr. Minami." He claims to be able to stop the sphere without using a nuclear attack. Back in Center City, Joey and the others are infiltrating the Skrugg's base, and in order to cause a diversion they split into two groups. The newly re-brainwashed Will and Nick appear before them. Joey has a plan to undo the brainwashing, but...

In order to destroy the controls for the spheres, Denton and Psy infiltrate the Skrugg's base, but they are quickly surrounded by the enemy and even with the guitar weapon can't progress any further. Then the Skrugg's leader, Kogorr, putting them in a desperate situation. But Joey and Heroman run in just in the nick of time to save them. It's time for the battle between the two powerhouses, Kogorr and Heroman, to get started!

Minami's crew prepare a machine called the MR-1 Prototype to fight against the ball. Meanwhile, Joey, despite his injuries, continues to help Heroman, but ends up taking more brutal hits from Gogorr. Heroman becomes infuriated and grows flames, unleashing his rage upon Gogorr, ripping off his wings and unleashing large blasts. Joey awakes and finds his controller isn't responding, he pleads with Heroman to stop him from killing Gogorr, returning him to normal. Gogorr resumes his attack, but is beaten by Heroman's Blast mode. Unable to accept defeat, Gogorr sets the base to self destruct. Joey's group hurries to the control room in order to stop the spheres before Minami gets a chance to use his machine. With their job completed, they barely manage to escape from the base before it explodes. Whilst Minami becomes infuriated over who interfered with his plan, a red eyeball is shown at ground zero.

As peace returns to Center City, the President is shown evidence concerning Heroman, who has been secretly help rebuild the city. Lina, who is depressed over Will leaving town due to his current state, tries to ask Joey out on a date, but keeps getting interrupted at every turn. A man by the name of Hughes questions Joey on rumours about Heroman. That night, some men kidnap Lina in front of Joey, forcing him and Heroman to take action. As Joey takes Lina back home, she is finally able to portray her request for a date. Meanwhile Axel Hughes, a secret agent for the president, reports the authenticity of Heroman.

As Agent Hughes continues his investigation concerning Heroman, Joey is visited by his energetic big sister, Holly, who had come back from her band tour to check out the alien situation in Center City, albeit three months late. Deciding to crash for a few days, Holly soon makes Joey's life a living hell for him. Hughes meets up with Minami to ask why he is around in Center City. Later, an explosion occurs and Joey and Heroman investigate, but it turns out to be a trap laid out by Hughes. Joey and Heroman run off and Hughes catches up with them until Heroman breaks some rubble that was about to fall on him and escapes under the cover of dust, though Holly manages to catch a glimpse of him. After they reunite, Holly plays a song at the pier before revealing she intends to stay longer, having seen something interesting.

As Joey goes on his date with Lina, they are stalked by Psy, Denton and Holly. As the date carries onto the beach, Joey's maths teacher, Vera Collins, inadvertently joins the stalking. Joey later catches onto their game and eludes them, only for the date to be interrupted by a report of Minami's MR-1 Prototype going out of control. Joey sends Heroman after the robot, who is actually being controlled by Minami to lure him out. Heroman manages to defeat the machine, but is caught on camera by a news helicopter in the process. As Joey returns to Lina, he gets Heroman to give them an unorthodox ride on the Ferris Wheel. Meanwhile Hughes, who had been watching the battle, discovers Joey on the scene.

Early one morning, a group of NIA troops, led by Hughes, enter Joey's house in search of him. Eight hours earlier, Joey was warned by Denton and got Holly to help him escape. After meeting up with Denton and Psy, they reveal that the government had been investigating Heroman, and covered up the previous day's incident to make Heroman look like the bad guy. With very little options, Joey, Denton and Psy prepare to leave the city and head towards Nevada. Meanwhile, the reporters for the All America Network who shot yesterday's footage are annoyed that they're report has been twisted to the government's will. With police checkpoints all over the city, Joey's group must resort to use Heroman for their escape. As Heroman distracts the majority of the cops, Denton and Psy push through the remainder. However, Joey and Heroman are then spotted by Hughes in a helicopter, but manage to lose them in an abandoned mine shaft.