The episode starts off with Vanilla stopping by the Chaotix Detective Office to thank the Chaotix for all that they did for her and Cream. Amy and Cream then bring a whole bunch of snacks to Tails to try and cheer him up.
When the giant seed finally reaches the final stage of its metamorphosis and starts sucking the life out of everyone except for Cosmo, she takes the Chaos Emeralds to Eggman, thinking that he'll know what to do. Unfortunately, Dark Oak attacks Cosmo, who drops the Chaos Emeralds into space. Thankfully, they close in on Sonic and Shadow, who use them to transform into Super Sonic and Super Shadow and attack the Metarex seed. But, once they destroy it, they reveal an even smaller planet with a gravitational force that could potentially destroy the whole galaxy!
Amy tries to rescue Sonic from the watery planet, but everyone else keeps her back, trying to come up with another plan. Then, Rouge comes up with a brilliant idea: use the Master Emerald to cut off the energy supply to Dark Oak! The team charges up the Sonic Driver with the Master Emerald and fires it at Black Narcissus and Pale Bayleaf, destroying them. Unfortunately, after this is done, the Master Emerald shatters, and it is revealed that the Metarex have sucked up all the Chaos Emerald's energy!
When Bokkun shows everyone Eggman's message (telling that the Metarex are starting to gather at galactic coordinates (0-0-0) because of a thousand-year prophecy), the gang starts lifting off to go beat the Metarex once and for all. Unfortunately, they leave Shadow behind! However, the Chaotix find Shadow and offer him a ride (for free, which is the surprising part) to galactic coordinates (0-0-0).
When the team discovers that Cosmo's brain is emitting a signal to the Metarex, they plan on trying to eliminate the signal, except that the signal is connected to the part of her brain that translates sounds and sight. While Tails and Cosmo are torn about this, Knuckles pushes for the surgery.
Shadow attacks the Blue Typhoon trying to kill Cosmo for reasons (at the time) unknown. Despite the efforts of Sonic, Tails and Knuckles to hold him off, Shadow reaches Cosmo. However, before he can harm her, Dark Oak's flagship arrives and steals the Chaos Emeralds, and Cosmo is revealed to have an implant that allows the Metarex to monitor everything she hears and sees. Along the way he nearly kills Sonic, Tails, Knuckles, and Chris
Yellow Zelkova attacks the Blue Typhoon, equipped with a special energy shield built by Dr. Eggman. Sonic attempts to stop him, but is unable to break through the shield. Picking up where they left off, Zelkova and Knuckles get into a fierce battle, during which Knuckles smashes Zelkova's knee and breaks the spurs on one of his gloves. Using cable from the Blue Typhoon, Sonic and the others channel lightning to overload Zelkova's shield. Zelkova's mechanical outer body is destroyed, revealing his flesh form beneath. Zelkova attacks, but is knocked into a nearby lava pit by Knuckles. Pale Bay Leaf informs Eggman of Zelkova's demise, mocking the failure of his shield. Shadow and Rouge find a fake Chaos Emerald at the top of the tree, but they hear groaning from its base. They find Leon (from the Resistance in Episode 68) being consumed by the tree, saying that the Metarex betrayed them. He also give Shadow a memory chip and says it's not too late to destroy the Metarex.
Following their battle with the Metarex fleet, Sonic and the gang are stranded on an alien planet with the Chaotix, who are running a cafe to pay for parts to their own ship. Dr. Eggman arrives looking for Sonic and the others, while Pale Bay Leaf waits in orbit to shoot the Typhoon down. Helping out Sonic and the gang, the Chaotix provide parts for their ship. However, Dr. Eggman provides the real assistance when he disguises the Crimson Egg as the Blue Typhoon and takes the full force of the Metarex attack. Pale Bay Leaf moves off, and no ambush awaits the real Typhoon once it takes off.
While traveling in the Galactic Cloister, the Blue Typhoon comes under attack from the Metarex fleet, led by the three surviving commanders and Dr. Eggman. Sonic attempts to attack from the Sonic Driver, but Dr. Eggman deploys a shield that not only repulses Sonic's attack, but causes an overload explosion that puts Knuckles out of commission. With Sonic and Knuckles both out cold, Tails assumes command reluctantly until Cosmo boosts his confidence. Coming up with a plan, Tails pilots the Blue Typhoon towards a black hole in the Cloister. Sonic and Knuckles recover long enough to deploy the Sonic Driver, reversing the black hole and allowing the Blue Typhoon to escape. Visiting the medical bay, Tails is praised by the injured Sonic and Knuckles.
In this episode, Sonic and the others find a meteor in space while searching for the Chaos Emeralds. Tails pulls it in, and they find it to actually be a space ship. Inside, small chao-like creatures called Marmolians are discovered and it is revealed that they have the Green/Cyan Chaos Emerald. The Marmolians and Sonic go back to their home planet, the Planet Marmolim, and Sonic destroys a diseased part of the planet that encased the Planet Egg. Amy thinks they have magic on the planet, so she tries to put a love spell on Sonic. However, it ends up backfiring, and instead works on Tails and Cosmo at the end of the episode, leading to the two embracing while watching the moon. This episode basically confirms Tails and Cosmo's relationship, while Amy gets extremely angry that she didn't catch Sonic.
Sonic is supposed to have a date with Amy, but he doesn't show up. So instead, she has a date with Sam Speed. Meanwhile on Eggman's old island base, Bokkun finds one of Prof. Gerald Robotnik's other creations: Emerl & tries to tell him to defeat Sonic. Bokkun opens the door, & he & Emerl walk to the tank. Sonic is trying to get to his date with Amy, but Bokkun stops him to free Eggman, Decoe & Bocoe from jail with the new tank. Can Sonic stop Bokkun & Emerl from freeing Eggman? Or will he be late for his date with Amy?
After the success of the sunshine balls, Eggman then tries to execute the rest of his plan. Sonic explains how Eggman eggmoon is moving to block, meaning Eggman set up the eggmoon as part of his master plan. Eggman then captures the president, and as he starts to make his own money, Sonic and Tails crash the X-Tornado into the white house and explain what happen while Mr. Tanaka and Topaz move the eggmoon out of the suns path. Sonic then set up a trivia challenge and traps Eggman by hitting him on the head with a big metal pan, and Eggman is sent to jail.
The Blue Typhoon is pulled into the Intergalactic Cloister, a strange region of space. Eager to do battle, Metarex Commander Yellow Zelkova launches an attack on the Blue Typhoon. Sonic and Knuckles team up to fight him, finding that Zelkova is too powerful for them. However, they then trick him into freeing the Blue Typhoon from a formation of space stalactites, and put him in line with the Sonic Driver cannon. They fire, and Zelkova is thrown back, but not destroyed. They then escape as he swears vengeance.
The Blue Typhoon encounters the Chaotix ship. Once aboard the Typhoon, Vector and Espio explain that they lost themselves in space and that their radio got broken. Tails agrees to fix their ship and he warns them that he doesn't want any trouble on the Typhoon. Tails begins his work when Cosmo brings him lunch. She reveals that she's planning a surprise for everybody. The Chaotix watch the scene and Vector notices the growing relationship between Tails and Cosmo. In order to thank Tails for fixing his ship, Vector decides to help him winning Cosmo's heart. At the same time, Tails unintentionally discovers Cosmo's surprise : she plans to throw a party on the ship. Cosmo is disappointed because it won't be a surprise for Tails now, but the little fox tells her that she won't be able to prepare everything all by herself. Also on the scene, the Chaotix propose their help and Vector takes it as an opportunity to throw his match-up plans. However, they all fail one by one. Espio believes that their relationship should develop naturally. After finishing the preparations, the Chaotix go get everybody to the party room when they cross Knuckles' path. Knuckles was used against his will in one of Vector's plans and he decides to take his revenge. Accidentally, they end up in the party room and they ruin everything. Arriving on the scene, Tails and Cosmo are disappointed, but Sonic says it's no problem and that they'll put everything back. He also thanks Cosmo for her party idea. The episode ends with Cosmo and Tails watching the stars outside in space.
The fight between Sonic and Dark Oak starts. Sonic directly attacks Dark Oak, but he instantly disappears: it was a hologram. Outside the fortress, a Metarex armada, led by Red Pine, is approaching. Surprisingly, the Red Pine army begins to attack their own fortress, while there still are Metarex inside. Shadow, Rouge and Chris are transported, via Chaos Control, inside the Egg Carrier. Chris finds a way to steal the emeralds found by Eggman and flees away by using one of Eggman's mini-ships. Shadow follows him and he stops him. The seven Chaos Emeralds are put together, transforming Sonic and Shadow into their super forms. Super Sonic and Super Shadow engage into a fight inside the fortress. At the same moment, a gravitational field is activated inside the fortress and it starts to destroy itself from the inside. The Metarex armada is destroyed, Super Shadow sees the Crimson Egg fly down to the center of the gravity feild and jumps in to follow it and stay with it, while the Blue Typhoon escapes with the power of the Master Emerald. However, during the event, the seven Chaos Emeralds disappeared.
Dr. Eggman discovers that the last two Chaos Emeralds (Cyan and Yellow) are located inside a huge Metarex fortress. The Crimson Egg and the Blue Typhoon arrive on location at the same moment. Eggman suggests Sonic to put their efforts together in order to enter inside the fortress. His plan: a little group will enter first and disconnect the fortress' security system, so the other ones could penetrate. Eggman sends Shadow and Rouge while Chris volunteers to accompany them. They enter with the help of Chaos Control. Rouge tries to get away from Shadow and Chris to get the Chaos Emeralds for herself. She reminds Shadow of the ARK and Maria, which causes Shadow to drop his guard as he has a sort of 'meltdown'. Rouge tries to escape, but is ambused by a Metarex. Shadow saves her and tells her not to run off. Chris finds the control room and they succeed in their job. Sonic & Knuckles penetrate in the fortress aboard the X-Tornado, Amy & Cosmo follow them and Eggman, Bocoe & Decoe are right behind. However, Eggman secretly installed a special device on each ship and he can take control of Sonic and Amy's ships. Eggman almost succeeds, but Sonic finds the emeralds first. The only thing: he is welcomed by an entire army of Metarex, led by Dark Oak, the Metarex leader, and the battle is about to begin.
The show opens with a sequence inside Cosmo's ship and ends when Scarship (see previous episode) destroys it, leaving Cosmo alone. Then, we find out the Blue Typhoon's crew on a new planet. It seems that there's a Chaos Emerald nearby. Tails, Knuckles and Cosmo follow the emerald's track to an abandoned city. Knuckles discovers a deep gorge. Lower, there's a cave. Tails and Cosmo enter, but Cosmo accidentally pushes a button which launches an avalanche and seals them inside the cave. Tails still receives the emerald's signal and he and Cosmo pursue their searches. Inside the Blue Typhoon, Amy receives a distress call from Knuckles and she informs Chris, Sonic, Cream and Cheese (who are all aboard the X-Tornado) of the situation. Inside the cave, Tails and Cosmo discover a big factory full of Metarex. They enter unnoticed and they find the Chaos Emerald inside a manufacturing plant of fake emeralds. They are found out by the Metarex, but they are able to escape with the White Chaos Emerald. Then, Tails fools the Metarex with special "fireflies". Tails and Cosmo are found retrieved by the Metarex and they steal the emerald from them. Tails engages a fight and Cosmo can take back the emerald. Tails is caught by a Metarex, but fortunelately for them, Sonic and the others come to the rescue. Tails and Cosmo also are starting to have feelings for each other.
The show opens with a fight involving a huge Metarex named Scarship and an armada of smaller ships. Scarship destroys every ship and he's assigned to a new mission: to destroy Sonic and Dr. Eggman. Inside the Blue Typhoon, everybody questions himself about Shadow's return. Aboard the Egg Carrier, Dr. Eggman finds out that Scarship is approaching and the battle engages. Eggman sends Shadow to destroy Scarship, but Shadow is unable to do the job. Rouge flees from the Egg Carrier, just before Starship sends a missile and seems to have destroyed it. Rouge informs the Blue Typhoon's crew of the situation and sends them images from the battle. Cosmo recognizes Scarship, it's the Metarex who destroyed her group's ship. Cosmo begs Tails to flee away, because she doesn't want to risk her friend's lives. However, Sonic and the others insist that they need to face Scarship. The battle starts and nobody gets the advantage. However, Sonic, Amy and Knuckles leave the ship unnoticed and they find a way to block Scarship's weapons. Scarship decide to destroy the Blue Typhoon by crashing into it. The Typhoon won't be able to get out of its way in time, but Shadow appears from nowhere and takes Scarship away. It appears that Eggman was able to escape from Scarship. Sonic and Shadow get inside Scarship and they destroy the engine room. However, Scarship won't ever surrender and it's about to self-destroy. Shadow is able to freeze time around it and Sonic defeats it with the Power Cannon.
The episode opens with a dream from Chris, where he remembers the events of Space Colony ARK and the loss of Shadow. He is awakened by Tails who tells him he has just found the signal from a Chaos Emerald. Inside the Crimson Egg, Rouge returns to the secret room she has just discovered and she spots the Red Chaos Emerald which is powering the strange capsule. She tries taking the emerald, but she launches an alarm and at the same time, she discovers that Shadow is currently hibernating inside the capsule. She's found out by Dr. Eggman. The Blue Typhoon follows the Chaos Emerald's signal to a dark, abandoned planet. Sonic, Amy and Knuckles search inside an old castle, while Chris and Cosmo look inside an ancient colony. Sonic's group quickly notices that the castle is a trap. In fact, it's an illusion created by a Metarex. This Metarex suddendly turns the castle into a sandtrap and almost catches Sonic. The Metarex attacks Sonic's group and Chris, who is in the Hyper Tornado. Sonic tries to counter-attack, but he is not able to beat the Metarex. Chris tries his luck and he fails too. At the same moment, in the Egg Carrier, Shadow awakens and he teleports himself to the fight place. He easily defeats the Metarex and he shows his presence to everybody. He looks at Chris, who just said Shadow's name, and he disappears with the Purple Chaos Emerald.
Chris' grandfather, Chuck, finds a way to teleport material objects to Sonic's world. The stuff is discovered by Vanilla and she asks the Chaotix Detective Agency to deliver it to Chris. She's also worried about her daughter Cream and she asks them to check on her. Vector accepts, but Espio tells him that they don't have any space ship. However, Chuck also sends a space ship to Sonic's planet and the Chaotix are on their way. Aboard the Blue Typhoon, Sonic and Knuckles are playing chess. Knuckles takes time before moving a piece, and Sonic decides to take a quick walk on the ship. Accidentally, Sonic slips from the ship and he diverts into space. Knuckles leaves the Typhoon to retrieve him. Inside the ship, Tails points out that another space ship is approaching and everybody is convicted that it's a Metarex ship. Vector, Espio and Charmy try, one by one, to get aboard the Blue Typhoon, but they are all thrown out from it. They take a little distance from the Typhoon temporarily, but Tails pursues them. He discovers a little house on the Chaotix ship and he realizes that it wasn't an enemy ship. Chris and the other ones apology and everybody unburdens the Chaotix ship from the stuff sent by Chris' family. Vector, having misinterpreted Vanilla's wishes, decide to leave the Blue Typhoon, taking Cream with them. Vector kidnaps Cream, but Cosmo sneaks along with them. Luckily, Sonic is back and he fights Vector in order to take the girls back with him. Finally, an agreement is settled and Cream gets back to the Blue Typhoon. The episode closes in Eggman's Egg Carrier, where Rouge finds a strange capsule in a secret room.
The Blue Typhoon detects two Metarex who just stole a Planet Egg on a jungle planet. Sonic destroys the biggest Metarex with the Power Cannon, but he is launched too hardly and he falls straight to the planet. He crashes on Dr. Eggman, who is already on the planet, and he takes the Green Chaos Emerald that the evil doctor has just discovered. Having landed on the planet, Tails and Knuckles get aboard the X-Tornado in order to find Sonic, leaving Amy behind. Amy desperately wants to find Sonic by herself and she enters into the jungle. She is accompanied by Cosmo, who wants to find the Planet Egg, and Cream & Cheese, who don't want to be left alone. Discovering he was left alone, Chris contacts Tails, but at the same moment, the X-Tornado spots a Chaos Emerald. Inside the jungle, Amy, Cosmo, Cream & Cheese struggle to find Sonic and the Planet Egg, but they are captured twice by the small Metarex who survived the previous fight. However, they escape and are able to take possession of the Planet Egg. Sonic is still running in the jungle with the Chaos Emerald in his hand and he is found by Tails and Knuckles. Dr. Eggman arrives and he steals the emerald from Sonic. Sonic and Knuckles prepare to fight, but the girl group and the Metarex appear. Eggman captures everybody (even the Metarex). The Planet Egg begins reacting and huge creepers wraps everyone. Chris arrives and Sonic is able to free himself and with a little help from Tails and Chris, he defeats Eggman. Finally, the Planet Egg gets back where it belongs and Sonic & his friends get back to the Blue Typhoon with two Chaos Emeralds in account now.
With the help of Chris' new program, the Blue Typhoon spots a Chaos Emerald on planet Freezy. Followed by Dr. Eggman's Crimson Egg, the Blue Typhoon approaches planet Freezy, but it's attacked by a Metarex and it crashes on the planet. Sonic, Chris, Knuckles and Cosmo decide to go get the Chaos Emerald with the X-Tornado. Rouge is also on her way for getting the emerald before Sonic. Everybody has to fight Metarex before reaching an ice palace, where the emerald is supposed to be located. Sonic's group find it, but it's sealed in a solid ice block. A more powerful Metarex appears and gets power from the emerald to become even stronger. A fight engages and Cosmo finds the way to defeat it with a laser beam. Knuckles finds the Chaos Emerald but before he gets it, Rouge steals it. However, Tails discovers that the emerald was a fake one.
After saving the planet in the former episode, Sonic and his friends are thanked in a feast. Dr. Eggman is watching the scene and he thinks about his next scheme to take away the Chaos emerald. Bokkun suggests a plan to Eggman, but the evil doctor doesn't notice that it has been elaborated by Rouge, who made her way to the Egg Carrier. Eggman soon finds Knuckles and he tries to persuade him that he tired to be a bad person and he wishes to leave the planet by using a Chaos Emerald. Knuckles believes him and he finds the others in order to take the Emerald they just found and to give it to Eggman. Sonic disagrees and both of them engage in a fight. Taking advantage of the situation, Eggman almost takes the Emerald, but he is stopped by Amy and the others. Then, a giant robot controlled by Bocoe and Decoe appears suddendly and it captures Cosmo. Eggman summons Sonic to give him the Emerald and he would let Cosmo go away. But at the same moment, a frog-shaped Metarex rises from the ground and it grabs the Emerald. Eggman let Cosmo go and he engages a fight against the Metarex. However, Eggman is defeated. It's Sonic's turn to fight the Metarex and, with the help of the Sonic Power Cannon and a Chris' trick, the blue hedgehog is victorious. The episode ends as Knuckles apologizes for being fooled by Eggman.
The Blue Typhoon is now on its way to a new adventure. Knuckles thinks that a Chaos emerald is nearby due to the Master Emerald's reactions. A planet is located and according to Sonic's guidebook, this is a dry planet. However, they find out that it's covered by water. Accidentally separated of the others, Chris & Sonic arrive to a Metarex base, where several Metarex await them. The fight is engaged, but Chris, wanting to help his friend, is unable to punch a Metarex without hurting himself. Eventually, Sonic is captured and Chris is able to escape. Informing Tails of the situation, Chris wants to rescue Sonic with the X-Tornado, but Tails insists that Chris won't be capable of his own. This leads Chris to question himself about his utility in their mission. Finally, Amy and Tails succeed to rescue Sonic with the X-Tornado, but Metarex attack the plane and by accident, Sonic falls straight toward the water. Chris arrives with another plane and saves Sonic with his own invention: hover shoes. The Metarex are finally defeated, the water retires from the planet and the Dark Blue Chaos Emerald is found.
Chris arrives in Sonic's world as his 12-year-old self. He makes contact with everyone, but Sonic faints shortly after. Apparently, the recent battle tailed him off. Back to Cream's house, Cosmo explains the Metarex goals and the consequences of the planet egg's removal. Cosmo also admits that she's the only survivor from her group, which was eliminated by the Metarex. Everybody (except for Knuckles, who's suspicious of her) agrees that the Metarex must be stopped and they decide to go into space to destroy the Metarex and to find the lost Chaos Emeralds. Luckily for them, Tails has just finished to build his new invention: a big flying fortress called the Blue Typhoon. Unfortunately, his new ship used to be powered by the Chaos Emeralds. Chris thinks that they could use the Master Emerald. Knuckles disagrees, but with some female persuasion, he finally agrees. At the same time, another Metarex is sent to the planet in order to destroy Sonic and the Blue Typhoon. A fight engages between the Metarex and Sonic & Knuckles. With the help of the Typhoon's primary weapon, the "Sonic Power Cannon" ("Sonic Driver" in the original Japanese version), the Metarex is destroyed. The Blue Typhoon takes off, but it is followed by Dr. Eggman and Rouge.
In the episode's opening, Super Sonic is fighting against a mysterious robot. Super Sonic is unable to defeat him and he sends the Chaos Emeralds away to avoid his opponent to take them from him. Without the Emeralds, Sonic loses his energy and he falls to his planet. Another robot (a Metarex) follows him. Back on the planet, Tails, Amy, Cream & Cheese watch the sky and assist to a meteoric shower. However, a space ship crashes near them, carrying a strange alien girl named Cosmo. After introducing themselves, they are surprised by the arriving Metarex who starts destroying the forest with laser beams. Tails, accompanied by Cosmo, starts fighting it with the X-Tornado and he's soon joined by Knuckles. Sonic (who was rescued by Dr. Eggman) arrives but they can't beat the Metarex. The last Metarex was able to finish his duty: which was to remove the "planet egg". Cosmo explains that the planet egg "is the lifeforce that sustains their world". Sonic, Tails, and Knuckles make a last effort to save the Planet Egg, but the Meterex escapes. Cosmo then tells Sonic that he is the final hope to save the galaxy. At the same moment, Chris (who is now 18) completes his new machine that will transport him to Sonic's world. It works, but Chris arrives in his 12-year-old body.
Sonic and his friends team up with 12 year old Christopher to collect all the Chaos Emeralds and defeat the evil Dr. Eggman.