Branded fugitives by Jonathan Rook, Jake, Nathan and Ricardo become Stretch, Wingspan and Omni-Mass once more when Dr. Don Robertson/ Multi-Farious rampages the city. The trio soon find out that Smokestack Jack, Circuit-Stream, Quick Charge and the Freak Sisters have escaped from Rook Tower as well. After a brief fight with Multi-Farious, Stretch calms him down and they find out some intel about the breakout before he walks off to think about his next move. Meanwhile, Blindstrike (recently revealed to be Riya Dashti, Jake's crush), incapacitates the Flex Fighters with smoke bombs and leaves them in the underground tunnels before pursuing Kari and Mari (The Freak Sisters) as they attempt to stage a bank robbery. Led by Dr. Racine Cleo/Dr. C, who reveals herself to have tried contacting them earlier, the boys arrive in her lab hidden within the old parts of Charter City underground. Like Multi-Farious, Dr. C deduces Rook staged a breakout to lure the Flex Fighters out of hiding. She volunteers herself and Blindstrike to handle the escapees and offers the Flex Fighters escape by handing over their uniforms. But the trio refuse, claiming that they could recapture the villains on their own. Dr. C agrees to help them, and the trio start their new campaign by apprehending Smokestack Jack at a nightclub in Old Town, where he dance-fights Madame Toussant and her gang. After Omni-Mass's plan to push Smokestack's air form around with a fog machine fails, Stretch turns on the a/c in the disco, causing Smokestack Jack to weaken into an unconscious state, while Omni-Mass disguises his voice and sends Rook Security an anonymous call to pick up Smokestack. Dr. C informs them that Quick Charge is attacking the power plant, and the trio heads there with a surprise partner: Multi-Farious. After the fight causes the building to flood with electrified water and breaks out into the streets, the Flex Fighters lure Quick Charge back inside, and Multi-Farious' pieces apprehend her, allowing Wingspan to leave another anonymous call to Rook security before the trio deduce an appointment Quick Charge mentioned she had was with Stretch Monster (Rook's monstrous alter-ego), and the trio agree to help Multi-Farious find Rook. After a brief skirmish with Kane and Delta Squad at Rook Tower, the group finds out Rook is hiding at the warehouse where the Flex Fighters got their powers, and Don was accidentally transformed into Multi-Farious. When he is found, Rook confronts them as Stretch Monster and almost ends up flattened by Multi-Farious before Stretch talks him out of it. The group soon learn that Rook had just finished a cure for Don's mutation, so after Stretch Monster manages to slip away, Don drinks the cure and explodes, turning into a stone statue of his human self before the shell breaks and reveals Don Robertson unharmed. He thanks the Flex Fighters for giving him his life back before they leave to help Blindstrike deal with the Freak Sisters at the bank. After witnessing Blindstrike trap them in an energy cage, Stretch interrogates Kari and Mari after Omni-Mass tries to seduce them and fails. The Freak Sisters reveal that Rook inserted chips into the necks of all the escapees, preventing them from leaving the city with a limited form of mind control. (This would later be referenced, as part of the canon parts of the story, in season 2 episode 9). After Blindstrike scans the chips on their necks, Dr. C receives the data and begins construction on a control device to round up Circuit-Stream and Quick Charge. Apparently, the latter escaped before Kane could break out of the tower and arrest her. The Flex Fighters soon find Circuit-Stream and prepare to fight him just as Quick Charge shows up in response to the use of Dr. C's controller. While Wingspan deals with Circuit-Stream in a stolen crane truck, Stretch and Omni-Mass distract Quick Charge, using her blasts of electric energy and Omni-Mass' fists to knock down the crane truck and electrocute Circuit-Stream until he falls unconscious. The Flex Fighters then engulf the two in a pyramid-shaped energy field, and retreat with Dr. C and Blindstrike in their camouflaged armored airship just as Kane and his Delta Team arrive on the scene. Impressed with their actions, Dr. C agrees to train them just like she trained Blindstrike, and that the five become allies in their crusade against Rook, much to the excitement of Stretch who proclaims "The Flex Fighters are back!" Meanwhile, after watching a live news report, Rook angrily vows to hunt down the Flex Fighters by any means necessary, no matter how long it takes, while his reflection of Stretch Monster shows up in the window as thunder and lightning clash.