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The game starts out with Zib telling the Hero/Rocka about subbmiting codes. After subbmitting a code of his own, he tells the Rocka to celebrate with a drink. Then, the alarms go off and Zib tells the Rocka that all of the villains have escaped and that the Hero should go investigate the Villain Storage.
Level 1: The Villain Storage Area
The Hero/Rocka is told how to pick up points, fire his gun, how to climb walls, how to upgrade a weapon, and about secrets. During that, he must defeat hordes of Arachnix Drones and henchmen to move on. Eventually, Rocka comes to Black Phantom, fighting him several times until finally being knocked unconcious, Black Phantom escapes, and Rocka returns to the Mission Management Station.
Level 2: Deep Sea Trench 675
The Hero/Furno goes down a sea sentry guarded path until he comes to a fork in the path. After choosing a path, Furno faces more sea sentries and finds Jawblade (either path will take Furno to him) and to defeat him, Furno must shoot him, his water bombs, and three cliffs to stun him. After cuffing him, Furno returns to the Hero Factory.
Level 3: Z'chaya Temple Ruins
The Hero/Evo starts out on a jungle path. If he goes backwards, he will find a rock pile that needs an upgraded gun to smash. If he goes to the right, he will fall off a cliff and find a group of pillars that can be jumped to find a blueprint. If he goes straight, he walks until he comes to a fork in the path. If he goes left, he gets an award, but if he goes right, he doesn't. If he continues down the left path, he will find a few rock piles that need an upgraded gun to blast through. However, if he continues down the right path he will come to a rock pile that needs an upgraded gun to destroy. Continuing down the left path, he will find a bridge that is raised, he then shoots it, making it fall and he climbs/crosses it after defeating the henchman on the walkways, he will come to a clearing were he sees Toxic Reapa, Toxic Reapa runs off while his henchman and arachnids attack, after defeating them, he follows Toxic Reapa through some ruins, he stands on a platform to make the gate that lead to Toxic Reapa raise. He follows the paths and goes through a waterfall to find Toxic Reapa who unleashes another barrage of arachnids. After defeating them, Toxic Reapa is faced, he shoots out toxic acids in puddles around him that can drain Evo's health bar. After cuffing him, Evo returns to the Hero Factory.
Level 4: Sigma Sigma Satellite
The Hero/Surge starts out on a meteor. Walking down a rocky path, he comes to many groups of Henchman. After defeating them, he advances to a teleport unit. After being teleported to the Satellite, he defeats many more groups of Henchman, and goes to another unit. He then battles and cuffs Splitface, bringing him back to Hero Factory.
Level 5: The Hive
The Hero/Breez starts out in a Hive, as the name depicts, she walks until she finds a group of henchman. After defeating them, she goes through many passegeways that lead to diffrent caverns, until she finds one that has three levers. She flips them, and runs to Thornraxx's cavern. After defeating and cuffing Thornraxx, she brings him back to the Hero Factory.
Level 6: Tansari
The Hero/Stringer starts out in the midst of a fog, where he follows a power cable that leads to computers that will shut off electricity gates, after shutting off all of the gates, he confronts, defeats, and cuffs Voltix.
Level 7: Kollix IV
The Hero/Stormer is on a motorcycle chasing Speeda Demon, Stormer then races up to him, dodging blasts and firing them at the same time as dodging stalactites that fall from the roof of caves. Eventually, he cuffs Speeda Demon and brings him back to the Hero Factory.
Level 8: Makuhero City
The Hero/Bulk starts out in the alleyways of Makuhero City. After he starts walking, arachnids start popping out of trash cans, walls, holes, etc. After defeating them, Core Hunter is seen. Following him, Bulk goes in circles until he has drained Core Hunter's health bar. Then, Core Hunter shoots open a gate, and runs through it, Bulk follows him and battles more waves of arachnids, he sees a tunnel and goes inside, where Bulk follows him again, draining Core Hunter's health bar as he goes. Core Hunter then uses a mechanism that opens a door. After going through it, he destroys the mechanism, opening another door, Bulk then goes through it, finding more mechanisms, he then opens the main door and continues. He then comes to a path that leads above ground. After defeating more arachnids, he follows Core Hunter, finds him, depletes his health bar, and cuffs Core Hunter, bringing him back to the Hero Factory.
The online version of the game relies mostly on keyboard controls. However, the mouse can be used to proceed through dialogue boxes or navigate various menus.
- Up, Down, Left, and Right are used to move your hero forward, backward, left, or right relative to the camera. Some narrow pathways can be followed using only the up and down arrow keys. The arrow keys can also be used to navigate some menus.
- W, A, S, and D can be used as alternatives to the arrow keys to move your hero or navigate some menus.
- Space Bar - The space bar is used to fire your gun when the cursor is on a distant enemy or object, or to use a melee attack when your cursor is on an adjacent enemy or object.
- Enter/Return - The return key is used to throw your Hero-Cuffs at a stage's villain after reducing their health completely. It can also be used as an alternative to the mouse to proceed through a dialogue box or navigate some menus.
- Henchman: Henchman are modeled on their boss, and usually look similar to them. Some Henchman are weak while some are strong.
- Black Phantom: His first wave of attacks is a launch of Arachnix, and then charge at the player, when he gets to the player he jumps and attempts to smash the player with his mace. His second wave of attacks, are mainly large swings of his mace.
- Jawblade: Jawblade utilizes mines, and will charge the player, to defeat him, one must bring a rockslide down on him.
- Toxic Reapa: Toxic Reapa will run around, spraying acid puddles around him as he goes. He also utilizes arachnids.
- Splitface: Splitface will slowly walk around, firing boulders and lightning as he goes.
- Thornraxx: Thornraxx will fly in circles around the player until he charges head on at the player.
- Voltix: The most complicated villain of them all. He utilizes an array of lightning powers. The player will have to turn six computers off to de-charge him, but even then, he will fire lightning at the player. After having his health bar depleted, he re-activates the six computers, he does this twice, every time making his lightning attack stronger, from a regular lightning blast, to a powerful lightning blast, to a jump so powerful that when he hits the ground, lightning fires in every direction. Tip: While he is charging his weapon or jumping, he is vulnerable.
- Speeda Demon: He will ride around on his motorcycle, firing with his extra arms backwards, until his health bar is depleted.
- Core Hunter: He will run around in circles, utilizing arachnids and mines as he goes.
- Rocka: Rocka is the first unlocked Hero, equipped with a Crossbow that doubles as a Plasma Gun, he is also equipped with a Energy Shield.
- Furno: Furno is equipped with a modified Plasma Gun.
- Evo: Evo is equipped with a Tank Arm that doubles as a Plasma Gun.
- Breez: Breez is equipped with a Blade, Plasma Gun, and Hex Energy Shield.
- Stringer: Stringer is equipped with a Sonic Blaster, that doubles as a Plasma Gun.
- Stormer: Stormer is equipped with a Power Sword and Plasma Gun.
- Nex: Nex is equipped with a Laser and Plasma Gun.
- Bulk: Bulk is equipped with a Missile Launcher and Plasma Gun.
- Surge: Surge is equipped with an electricity sword and a plasma gun.
- With some computers the Hive level moves in slow motion.
- All the characters with tubes in set form are missing their pipes in the game.