Shortly after returning from the Floating Island, Sonic the Hedgehog has set plans under way to evacuate Kintobor's Laboratory. Since Doctor Robotnik spent time as a prisoner there, he now knows its location and has come back, armed with a Squeeze Tag Machine and several Badnik guards. Sonic orders Tails to take the bi-plane and Amy Rose and go to the Rendezvous point. Porker Lewis is having a lot of trouble getting the Kintobor Computer back on to the Mobius Ring it came from but time is running out; Johnny Lightfoot informs everyone that Robotnik has found them and is on his way. On the Floating Island, Knuckles the Echidna is trying to get into Robotnik's Launch Base Zone but a Trooper is guarding the entrance. The echidna lashes out, still furious that Robotnik tricked him. He plans to rid all traces of him from the island, starting with the Death Egg...
The entire laboratory begins to shake, suggesting Robotnik has hit the outside. With Porker still stuck working on the computer, it's down to Sonic and Johnny to buy him some time. Rushing down to the underground entrance, the Freedom Fighters are soon attacked by the breaching Robotnik and his Tunnelbot-Grounder-Crawlton army. Johnny is quickly captured in the mech's large fist but Sonic frees him with a Spin Attack. Robotnik reveals he should be supervising the repair of the Death Egg but couldn't resist personally attacking the hide-out. He also plans to return to the Launch Base before Knuckles realises it's still operational. Sonic launches another Spin Attack but Robotnik retaliates with his massive arm. This time, instead of attacking directly, Sonic begins to Spin Attack the roof and walls around the Machine, prompting a rockfall to bury Robotnik for the time being. With Robotnik preoccupied, Sonic and Johnny return to Porker who has been successful in saving Kintobor. Unfortunately, all the exits are now sealed! Breaking free of the avalanche, Robotnik contacts Grimer, who reveals that Knuckles has been in the Launch Base Zone but was killed by Troopers. In actuality, Knuckles has Grimer hostage and told him what to say to Robotnik.
Robotnik bursts into the main control room, intent on destroying the three heroes. Sonic insists that a few more Spin Attacks will defeat the Squeeze Tag Machine, but he won't get the chance; the roof begins to cave in again and Knuckles appears, much to Robotnik's surprise. The echidna smashes open the glass, leaving Sonic to Spin Attack the roof of the machine and send Robotnik flying. With his plan in trouble, Robotnik orders the Badniks to defeat the four of them. Sonic watches as Knuckles seems to be fleeing, but he's really just making his way outside to give them more space in the fight. As the Badniks follow them, Sonic, Knuckles and Johnny rip into the foes as Robotnik flees in his Egg-o-Matic. Trooper reinforcements arrive but the foes are soon dealt with. With the fight over, Knuckles reveals he felt it was his fault that Robotnik found his secret base and wanted to help but Sonic doesn't need anyone's assistance. Now that Robotnik is gone, Knuckles commandeers a spare Egg-o-Matic and flies off home.
Soon, the three heroes meet up with Amy and Tails, Amy worried sick about Sonic's lateness. The five of them clamber into a circus labelled "Bob Beaky's Travelling Circus" and Sonic is urged to get into his Bob Beaky disguise. Soon, the caravan comes across a Trooper patrol, one of them asking driver Porker if he's seen the Freedom Fighters anywhere. The robots look into the caravan but only see four circus performers, so waves them on. As the heroes begin their life of travel, Sonic rips into Johnny's ridiculous moustache.
- Bob Beaky's caravan is seen for the first time. Bob has also seen a redesign from his old wintery clothing to a ringmaster's outfit.