To get inside Cyclonia during its "Ultimate Warrior Championships," the Storm Hawks enter Junko as one of the colorful competitors. Things quickly get out of hand - especially when Junko gets a little too much into character.

Robberies have been occurring all over Atmos, and have somehow been linked to the Storm Hawks! They go looking for the culprits while desperately trying to prove to their friends that they are innocent.

The space race is on, and Cyclonia has a head start. After discovering Ravess is commanding a battle platform high in the Stratosphere, the Storm Hawks must go higher, faster and farther than ever before to stop her.

Stuck in the unforgiving Wastelands, the Storm Hawks must fend off an old Cyclonian rival bent on revenge. Meanwhile, Junko hopes to impress the tough as nails Wallop miners they went there to rescue.

Stork and Leugey get stuck together when Stork swallows a Gravatron Crystal. Now the Storm Hawks must find a way to get the two unstuck without Repton knowing about it.

The Storm Hawks have to deliver a weird container and are told not to open it. But Finn's curiosity gets the better of him and he opens the container, which shoots out a weird gas that turns Finn into a monster. Stork creates a cure, but gets a little carried away trying to get Finn to take it.

Piper meets a princess who looks exactly like her. The princess wants some adventure in her life, so she switches places with Piper and joins the Storm Hawks. But Piper gets into trouble when the princess' kingdom is invaded by a group of creatures know as the Nightcrawlers.

Carver, the former Sky Knight, claims that he has reformed and wants to join the Storm Hawks. The Storm Hawks really believe that Carver has changed, except for Aerrow, who thinks that Carver hasn't changed one bit. He's finally right when Carver tries to convince his friends that he's under Cyclonian mind control.

While on a trip to Terra Neon, the Storm Hawks accidentally leave Radarr at a rest stop. Now Radarr must find a way to get back to the Condor while avoiding Cyclonians and a chicken that has a crush on him.

As part of volunteer work, Stork takes a group of young Merb scouts on a camping trip. But things go totally wrong when Stork and the scouts land on the wrong terra, which is full of vicious creatures. They also have a run in with Snipe, who is testing a new weapon of his.

The Storm Hawks end up at Sky's End, an uncharted part of Atmos which is believed to be home to dragons. They meet a group of young dragons and try to protect them from the Murk Raiders who want to slay them.

After winding up in a body cast, Aerrow must spend five days in bed while his wounds heal. This proves to be difficult when Master Cyclonis invades the Condor.

The Dark Ace stumbles upon a powerful suit of armor that is powered by crystals. Now the Dark Ace goes on a power hungry rampage, sucking up every crystal he can find and it's up to the Storm Hawks to stop him.

The Storm Hawks respond to a distress call from the bottom of Terra Aquanos to rescue the Neck Deeps. At the bottom they find monsters which have been released by I.J. Domiwick from a sealed cavern. In this cavern are supposed endless tunnels that lead to everywhere throughout the Atmos, even the fabled "other side". While the Storm Hawks and Neck Deeps try to seal the cavern, Domiwick escapes, but only delays their plan and swims into the cavern before Finn reseals it. However, just as the Storm Hawks head for the surface, one of the monsters punctures the Condor, causing it to flood. All but Aerrow abandon ship, Aerrow having giving his breather to Piper after Domiwick stole hers. Aerrow manages to make it to the surface while riding atop the monster, now called "Bessie", to satisfy Stork's belief that it exists. In the last scene, Domiwick is seen crawling up onto shore on an unknown land.

With nothing better to do, the Storm Hawks answer a distress call from a very small, almost unnoticeable terra, where they meet a nerdy boy named Noob. Noob is their number one fan and president of the Storm Hawks fan club. Noob manages to talk his way onto the Condor, quickly becoming an annoyance to the Storm Hawks. Noob wants to see them fight Cyclonians but the Cyclonians haven't been active for weeks, which Aerrow finds suspicious. Cyclonis is planning something that requires many rare warp crystals, that she sends her Talons to collect. While playing on Finn's Skimmer, Noob nearly falls into the Wastelands. The Storm hawks decide it is time for him to leave, but he refuses to, believing that they are testing him. Finn finally snaps and hurts his feelings, which convinces Noob to leave. Noob soon sends another distress signal, but the Storm Hawks don't believe him, even though Ravess and some Talons are actually attacking the crystal mines on his terra. Ravess captures Noob and interrogates him. The Storm Hawks, feeling bad, head back to his terra. Meanwhile, Ravess accidentally reveals Cyclonis' secret plot. The Storm Hawks arrive and rescue Noob, who possesses three warp crystals. Noob drives his trailer into Ravess and the warp crystals activate, sending her to Master Cyclonis. Noob then tells them about Operation Exodus, Cyclonis' secret mission. Noob realizes that he shouldn't obsess with the Storm Hawks and whips out a trailer dedicated to the Absolute Zeros.

The Colonel has lost his favorite pet, "Mr. Fluffykins", who ends up on the Condor and causes havoc. The Colonel track Fluffykins to the Condor, and out of gratitude for "rescuing" his pet gives them his services for the day, as part of a gangster code. While Finn plays along, Stork believes that Fluffykins really ran away. The Storm Hawks take advantage of this to keep him so busy that he won't be able to do his regular crimes. His jobs include working in a soup kitchen, picking up trash, exterminating bugs, giving away some of his money, and releasing prisoners from Cyclonian prison. The Colonel soon realizes that they never rescued Fluffykins and plans to take revenge on them for humiliating him. The Colonel tries to unleash Fluffykins on Piper, Stork and Junko, but Fluffykins stops when he sees a flock of his own kind. They realize that he just wants to be with free. Fluffykins tries to fly but his restraining collar prevents him from doing so, causing him to fall into a pit filled with lava. The Colonel reluctantly frees the Storm Hawks and uses his web to lower Radarr to save Fluffykins. The Colonel states he is again in their debt, and Piper wants him to release Fluffykins. Colonel sadly releases him and says goodbye to his beloved pet.

After a futile search for Operation Exodus, the Storm Hawks decide to take a vacation on Terra Tropica. However, a tsunami separates Aerrow, Finn, Junko, Piper and Radarr from Stork and the Condor, who is ambushed by some natives. Aerrow heads to find Stork with Radarr while the others search for food and make shelter. Stork manages to scare off the natives with an amateur magic trick and makes his way to the Condor but it confronted by the same natives, only angrier. They chase him throughout the jungle. Stork flees into an ancient temple which the natives won't enter. While inside, Stork finds a strange door guarded by a giant crystal golem. Stork runs out of the cave followed by the now frightened natives and the angry golem. Stork makes it to the Condor but finds it guarded by natives. He uses one of their masks to impersonate them to get by. He flies the Condor to his friends and picks them up before a second tidal wave hits. Stork tells them of the natives, the golem, and the and strange door but they don't believe him. In the final scene, Cyclonians are seen heading to the same temple.

Master Cyclonis leaves on a secret mission to retrieve the doorway Stork found in the previous episode puts Ravess in charge in her absence. Ravess abuses her power at Snipe's expense, so Snipe stages a mutiny with the help of the commander from "Radarr Love" and takes control of Cyclonia. More concerned with his own amusement than running Cyclonia, Snipe ignores the commander that helped him and carelessly orders the Talons to shoot down anyone that approaches, which happens to be Repton and the Raptors. Angered by Snipe's actions, Repton successfully overthrows Snipe, helped by the commander Snipe snubbed. Now in charge, Repton prepares the fleet for an attack. The rest of the Raptors decide to overthrow Repton because of how he treats them and end up driving their ship into Cyclonia. In his attempt to punish them, Repton accidentally locks himself and the Raptors in a cell with Snipe and Ravess. Lugey, however, is left outside and takes charge, just as Master Cyclonis returns. Still needing their services, Cyclonis forgoes punishing the Raptors or Snipe, but has Ravess banished for her incompetence.

The Storm Hawks have a night to watch a movie on their adventures. Each of the Storm Hawks get a chance to show a video about them. Finn makes a movie about himself, Piper makes two videos (one about crystals and another about places in the Atmos), Junko shows a movie about each of their Skimmers, Stork shows his top ten fears (things to avoid in the Atmos), and Aerrow shows what it's like to be a Sky Knight. Everyone bails at the last minute when Junko suggests to watch his experimental film where he sleeps for hours.

This episode serves as a prequel to the series. Aerrow, Finn, Piper and Radarr are orphans living in a fortress on a small terra, which is threatened by a Cyclonian Youth Squad, which Junko is a part of. Three men approach Aerrow and give him a key and map to the Condor, stating that he is the last descendant of Lightning Strike, leader of the Storm Hawks, and thus inherits leadership. However, because of them Aerrow and his friends are captured. The leader of the Youth Squad radios Snipe and is told to throw them into the Wastelands. Junko volunteers to do it, but lets them go when the others are not looking, as he does not want to be a bad guy. They manage to find the Condor in the Wastelands, and it has already been repaired by Stork, who has lived there for years trying to find the key. In possession of items they both desire, the two sides team up. Stork takes them to the hangar bay, where they find all of the Skimmers and weapons used by the original Storm Hawks. The Storm Hawks head back to their terra to reclaim it and battle the Youth Squad. Junko switches sides upon seeing the Condor. Snipe arrives and gives a leech crystal for the leader to attach to the Condor. Aerrow manages to get it off just before the Condor plunges into the Wastelands. After regaining their home, Aerrow feels as though it can no longer be their home knowing what they now know about the Storm Hawks. Piper then states that the Storm Hawks were special because they didn't have a home terra; they protected everyone. The same three men appear again and contemplate on their future stating that the boy will be a Sky Knight, and whether the "girl" is the "one"; only time will tell. On Cyclonia, Master Cyclonis is seen moving her grandmother's throne and working on her Storm Generator.

While the Storm Hawks return to Tropica to investigate the temple Stork found there, Finn and Radarr are sent off on a solo mission for cooking crystals so Finn doesn't compromise their stealth mission. Finn lands on a Western-style terra and enters a salon, where he angers a four-armed bandit and is challenged to a draw. Finn defeats the bandit, earning the respect of the townspeople. The bandit swears revenge on Finn. Elsewhere, the Storm Hawks reach the temple, only to find Ravess there instead of the doorway or the monster. Disgruntled by her banishment, she tells them that the door leads to the far side of Atmos, but without the key Cyclonis cannot open it. Back on the western terra, Finn's ego gets the better of him and he makes his own squad called the Ultra Dudes, teaching them useless tricks. When the bandit returns with his Murk Raider allies, Finn confesses that everything he taught them was useless. The Ultra Dudes, however, still have faith and want to defend their home, but naturally cannot do much against the Murk Raiders with what Finn taught them. Finn comes to their rescue after some guilt tripping from Radarr. The Ultra Dudes manage to defeat the Murk Raiders with the help of the townspeople. Finn challenges Captain Scabulous to a draw, which Scabulous cheats at, and wins when the townspeople step in. Finn returns to the Condor and is glad that he is not the leader of the Storm Hawks, seeing as there is so much work to it.

Junko has been summoned back to his home on Terra Wallop and Aerrow insists that they accompany him. They head to see the chief who tells him he is taking over the family business: underwear retail. Junko cannot refuse as it will bring shame to his family. Piper and Aerrow head to find Junko's Uncle Dilly, the previous owner, and discover Cyclonians. The chief reveals that he invited the Cyclonians as a part of a treaty, as he expects them to win the war and wants to be on the winning side. Junko challenges the chief to a battle after failing to convince him that the Cyclonians are evil. During the match, Junko tries to reason with the chief, but the chief won't listen. Junko realizes the chief won't fight the Cyclonians because he is afraid to stand up to them, and manages to subdue the chief by tricking him into knocking trees onto himself. Junko refuses to deliver the finishing below that would solidify his position as the new chief. As the Storm Hawks depart, Junko states that strength means nothing unless they have the courage to use it for good. Other Wallops contemplate on Junko's words of courage and decide that just because their chief supports Cyclonia, they do not have to. Junko's words have inspired them to create the Wallop Resistance.

The Raptors destroy the Condor, and a Cyclonian attack on the Storm Hawks scatters the team. Piper lands on Gundstaff's terra, who decides to help her after revealing that the Cyclonians have also taken his family. Finn lands on a Blizzarian's garbage truck. Junko fights off Cyclonians with the help of some wrestlers. Aerrow is told by the three guardians from "Origins" and Arygyn that the future of Atmos doesn't include him, but Arygyn assures him that he will do fine. Finally, Stork follows Repton to Terra Bogaton and single-handedly liberates it during his anger/revenge fit on Repton for destroying the Condor. Grateful for his actions, the Bogaton scientists decide to rebuild the Condor. Snipe is banished for failing to destroy Aerrow.

While reconstruction of the Condor gets underway with countless volunteers, Aerrow and Piper check out a report of Cyclonian activity in the Forbidden City. There they find Master Cyclonis and the Dark Ace summoning the spirit of the Oracle, in order to divine the location of the Oracle Stone, which is the key to Master Cyclonis' far side door. Said stone was given to Piper as a gift by Aerrow, and remains in her possession. When Cyclonis threatens to destroy the Oracle spirit, Aerrow jumps in and gives her time to escape. During the battle, Cyclonis takes the key and Piper finds herself displaying new skills that give Aerrow power, like super strength, which Master Cyclonis is also capable of. However, the Dark Ace and Cyclonis escape. Aerrow and Piper head back to Bogaton where the workers have completed the Condor. Piper worries about her new skill, saying that it feels dark, as does the Dark Ace, who fears that Piper may become as powerful as Cyclonis herself. Cyclonis remains unconcerned, convinced that Piper will destroy herself before she can master the power. In the final scene, Cyclonis opens the door to the far side and walks in.

Using her far side door, Master Cyclonis arms her Night Crawlers with crystal technology from the far side, making them far superior to any force in Atmos. Aerrow leads a united Atmos straight into Cyclonia for the battle to end all battles. Piper learns from Cyclonis that her new power, known as the "Binding", is evil and will turn her evil if she masters it. Piper insists on developing the power anyway, despite Aerrow's misgivings. Aerrow's united force manages to defeat the first wave of regular Cyclonians, but is vastly outgunned when Cyclonis releases a second wave of Night Crawlers. Furthermore, she has equipped her terra with levitation pontoons, turning it into a flying fortress.

In only a few weeks, Cyclonis conquers all of Atmos. Every Sky Knight is trapped in a crystal prison and their vehicles scrapped. Only the Storm Hawks remain, playing childish pranks on Cyclonis. Piper is in bad shape, the Binding slowly weakening her despite not using it. Cyclonis, tired of their resistance, threatens to destroy Terra Atmosia, and the Storm hawks surrender to prevent it. This turns out to be a ploy to reach the crystal prison, which Aerrow shatters with help from Piper. The freed Sky Knights attempt to shoot down Cyclonia with stolen Skimmers, but cannot penetrate the shielding on the levitation pontoons. Stork and Finn, however, discover that the crystal technology the Night Crawlers wear is allergic to Radarr's fur. Meanwhile, Aerrow and Piper face Cyclonis and the Dark Ace. Already quite weak, Piper's ability to empower Aerrow ultimately gives out. However, when Aerrow insists they will die together, the Binding flows from him and into her, restoring her health and empowering them both. Unable to defeat them with her ordinary skills, Cyclonis draws power from her far side crystal to empower the Dark Ace, but gets carried away and destroys him. The resulting energy release destroys the far side crystal, allowing Finn and Junko to disable the pontoons. Cyclonis escapes through the door to the other side while the Storm Hawks follow. The end scene is narrated by Starling, who relates that it has been six hours since their victory. They raise up a flag of the Storm Hawks, the bravest heroes Atmos has ever known. Meanwhile, the Storm Hawks make it to the other side filled with new creatures and places. The story continues in season three of Storm Hawks at the other side of the Atmos.