The cartoon opens with Sonic cruising through the Great Forest on a beautiful, sunny day. Suddenly, Bunnie and Tails appear in his path and flag him down. He comes to a sudden stop. With concern in his voice, he asks what's going on. But nothing is wrong; they just have a surprise waiting for Sonic. Sonic loves surprises, and allows Tails to blindfold him. Bunnie can hardly contain the secret, confident Sonic will be thrilled. They lead Sonic along the path for some time. Sonic grows impatient with all the slow walking they're doing, but Bunnie calms him down by telling him that they are almost to the surprise. They leave the undergrowth of the ancient forest and enter an open meadow. Sonic anticipates something magnificent as Tails removes the blindfold. Rotor, Sally, and Antoine stand before him and a home-built minijet. He is not impressed by the gangly looking invention. But he tries to hide his disappointment by asking what it is. It seems everyone else is excited about the plane, as Antoine and Tails comment together how "past cool" it is. Sally declares its name -- "The Freedom Stormer." Trying to sound appreciative, Sonic weakly says, "It's ... really great." Sally then goes on to explain why they built it. They will fly in it to reach the ancient city of Mauga to find the Secret Scrolls. Sonic wants to know what these scrolls are. Sally tells how her father had once told her about these, how they had great powers contained within their writing, and how no one had ever found them. Sonic cannot help but point out that is why they are "secret" scrolls. But Sally is confident they can find them, but Sonic isn't. No longer can he contain his low opinion of the plane, calling it an "air jalopy." Sally points out that Mauga can only be seen from the air and that the plane is not a jalopy. She goes on to reveal how much research she has put into this endeavor to persuade Sonic that they can succeed. However, Sonic is not convinced. Rather irritated with his skepticism, Sally demands why he thinks the mission will be a failure. He says that there is no way that the plane could survive a Stealthbot attack; so Sally counters that they will fly at night. Sonic then points out that Robotnik's radar will still detect them even at night, but Sally says that they will fly below the radar. Sonic doesn't care; he doesn't like the plan and tells her that he will have no part of it. Sally is adamant and says that they will go, even if Sonic stays behind. At this stubborn declaration, Sonic finally gives in and agrees to go with them, but he will not fly in the plane. Instead of flying, he will follow them on foot.
Later in the evening, the Freedom Fighters are ready to head out. Rotor, as the pilot, starts the engine and performs a quick check of the aircraft's systems. In the rear seats, Antoine and Bunnie wait to take off. Antoine is quaking, and Bunnie cannot help but ask if he is scared to fly. Trying to act bravely, he clears his throat and proclaims that he is not scared of anything. Rotor has finished his safety check and tells Sonic to let the plane loose. So he unties the cord that holds the plane to a tree and unchocks the wheels. Sonic wishes them luck as the plane rolls progressively faster downhill. Antoine is clutching the plane with white knuckles as he proclaims how much he loves to fly. The plane reaches the bottom of the hill and hurdles off a cliff into open air. But something is wrong -- the plane is not flying but diving down into the canyon. The throttle is locked up. Sally and Rotor struggle to pull back the lever as they continue plummeting down. No a moment too soon, the lever gives and the plane soars upward out of the canyon. Sonic, knowing that his friend are safely out of danger, begins to follow.
The plane has flown over quite a distance. Antoine wants to know how much farther to the city. Sally tells him that it is beyond the next few mountains. They fly over them and, as she said, there is Mauga -- the city on a hill. The sun is rising as Rotor descends to land the plane. There is a single place to land, but it is not very long. Bunnie tries to encourage Antoine by describing the "ground [that is] rushing up to meet" them. But this only freaks Antoine out more. The plane touches down, but the runway in not just short, but too short! Antoine is screaming out his lungs as the plane barrels forward toward the cliff that marks the border of Mauga. But the Hedgehog is not far behind. He grabs the cord on the back of the plane and pulls back as hard as he can. The plane slows down and comes to a stop just before it reaches the edge of the cliff. Everyone is a little startled (except for a very startled Antoine) but all right. Sonic comes to see if they are fine as they exit the plane. Bunnie tells Antoine that he looks a bit green and Sonic concurs. Antoine tries to deny it by declaring that he feels his finest but runs off very nauseated. Sonic isn't done yet. He wants an ego boost. Sally, in frustration, just walks off. The companions begin to explore the ancient city. They are amazed by the magnificence of the ruins, especially a giant arrow-shaped stone that has some writing inscribed on it. Sally declares that it is the Arrow Stone which marks the entrance to the city. While they look at it, a mysterious wind begins to blow. Paranoid, Antoine asks what it is. Sonic takes this chance to scared him by telling him it's the sound of a monster. But Sally is busy translating the writing with Nicole. It is a cryptic riddle: "We do not see things as they are; we see things as we are." No one knows what it could means but it doesn't matter: the entrance to the city is before them. A dense, tall hedgerow surrounds the whole city, blocking the entrance. But that doesn't stop Sonic. Curling into a super spin, he cuts a path right through the bushes for his friends to pass through. The city of mysteries becomes yet more mysterious when the freshly cut hedge grows back to fill in the path Sonic cut. However, there is no time to investigate. They continue on their mission. In front of them is a solid block wall that checks they're progress to the temple where the scrolls are.
There is no way over so they hunt for the first marker: The Chair. But the noise returns. Sally remarks how it begins every 2.1 minutes. This time it's more than just noise but a gale. The Freedom Fighters have to take refuge behind a stone pillar. As they stand in its shadow, another mystery of the city is discovered. The shadow makes them invisible. Yet again, there is no time for curiosity as they continue to look for The Chair.
Farther along the wall, they discover more strange writings. The translation reveals another enigma: "What one cannot achieve in learning, one will achieve in the light of day." Unclear to its meaning, they continue their search for The Chair. Nicole gives information concerning the markers and their significance to Mauga philosophy. The two markers test one on the Three Degrees of Awareness: intelligence, spirit, and courage. Only the worthy, according to the Nicole, cannot successfully complete these tests. Bunnie is confused though how there are three tests on the Degrees of Awareness but only two markers. Unfortunately, Sally has no answers and so continues with more questions than answers.
After hours of searching for the elusive Chair, they stop to rest. Something catches Sonic's eye: a pile of rubble that looks a bit odd. As the sun rises in the sky, its rays pass through a hole in a nearby pillar and shine on a single object in the pile. "Yup," Sonic says, "definitely a chair." Sonic can't help but give himself a pat on the back. On The Chair, Sally discovers a copy of the writing they found on the wall. Unsure what to exactly do, they just decide to sit on the chair. When nothing happens Sonic gets impatient and begins tapping his foot against it. Like a rocket, The Chair blasts upward without warning over the wall and lands on the other side, right in front of the temple. They dash into the temple only to be confronted with another puzzle: there are two sets of scrolls! Sally reveals to them that one set is a fake and that if they take the wrong one the temple will explode. But which one is real and which is fake? The only clues given are the containers of each set. One is a simple twig structure; the other is a beautiful vase of glittering gold and jewels. Bunnie reminds Sally about the strange writings, and suddenly it becomes clear. "We see things as we are," triggers a thought train in Sally's mind. She tells them how they overcame the first test with intelligence. Then, Bunnie replies, this test must be for spirit. And they are Freedom Fighters -- those who live by conviction and spirit. Universally, they agree that the twig container is the way to go. With mustered confidence, Sally slowly approaches the container. It begins to glow with a fierce intensity and, with a final pulse of blinding light, releases two scrolls. It was the right one! Sally gives one to Bunnie and unrolls the other. Nicole translates that the scrolls reveal the Seven Wonders of Mobius -- powerful and natural wonders. The first is the Breath of Mobius, a windtunnel located within the city of Mauga. It is responsible for the regular wind gusts with in the city.
But they aren't through yet with all the tests for one remains: the Test of Courage. A door slides away across the room revealing an unexpected 'guest': Robotnik! He, along with Snivley and SWATbots, enters the room and demands the scrolls. "Ya snooze; you lose!" replies Sonic. Sonic asks for a second to discuss the problem with Sally, but they really plan an escape. "I'm waiting, Hedgehog," declare the despot. "Hey! That's mine line!" retorts the blue hero. He goes into a super spin to stir up all the dust on the temple floor. While the rising cloud blinds Robotnik and the SWATbots, his friends sneak away into a tunnel. The SWATbots are sent to hunt for Sonic when the dust settles, but Sonic returns to insult the fat man one-on-one. Robotnik tries several times to shoot him but Sonic is too fast. Figuring that he's embarrassed Robotnik enough, he blasts out of the temple into the city. But Robotnik won't let him get away that easy and releases his new surveillance orb -- the Stealth Orb.
In the tunnel, Sally, Rotor, Bunnie, and Antoine are lost. Antoine accidentally finds the way out when a spider scares him. He falls against the wall as he tries to get away, and a secret door opens in the wall, revealing the way out of the temple. Antoine tries to take full credit for the discovery, but everyone is too excited about getting out that they ignore him.
Sonic is doing his best to lose the special orb but is unsuccessful until he performs a 180-degree turn and hides behind a pillar. He has a few minutes before the orb finds him again and the 'bots converge on his position. He meets up with the gang. Sally suggests that he hide in the wind-tunnel but cautions that the 175 mph winds will not just blow away Robotnik and the 'bots but him as well. Of course, Sonic is not worried; "the Hedgehog can outrun any wind!" They have no more time to discuss the plan because the orb returns. Sonic blasts off to the Breath of Mobius, making sure that the orb is following. He hides behind a pillar near the opening to the tunnel and waits for the enemies. When they show up, he runs into the shaft and sits in a nook on the side. Now he waits. Robotnik tries to coerce the hedgehog out to no avail. Sally is counting down the seconds. A faint breeze hisses from the tunnel. Before Robotnik and Snivley realize what's happening, the wind blasts. The tremendous force of the wind hurls Robotnik, Snivley, and all the SWATbots into the air and off a cliff. Sonic then shoots out of the hole himself, but with the help of a power ring, he outruns the wind and lands safely on the ground. That's when it hits them, Robotnik is dead; they've won!
That evening, the Freedom Fighters are packing up to head home. Sally asks Sonic if he's coming along in the plane. He says that he will under one condition: he flies the plane. Well, against their better judgment, they let him pilot the aircraft. They are quickly sorry when he performs a series of loops and barrel-rolls. As the fly off into the evening sky, victorious over Robotnik after a decade of war, a gloved hand reaches up and grasps the lip of the cliff. Then another appears, followed by a pair of glowing red eyes. Robotnik, against all odds, had survived, as well as his nephew Snivley who comes up beside him.