In the futuristic Charter City, high school students Jake Armstrong, Nathan Park and Ricardo Perez accidentally break into Rook Unlimited, owned by industrialist and Charter City benefactor Jonathan Rook. The three are dosed with flexarium, a malleable and powerful material, and gain elastic based superpowers. While fleeing from the authorities, the three take on disgruntled Rook employee Dr. Don Robertson who has transformed into a strange monster dubbed Multi-Farious.

Rook, impressed with Jake, Nathan and Ricardo's heroics, decides to hire them as Charter City's official superhero team, The Flex Fighters. The team decide to keep their identities secret, even from Rook, as they gain the codenames Stretch, Wingspan and Omni-Mass. Robertson, who escaped their fight from the previous episode, is still on the loose and the Flex Fighters must prove that they can handle the situation, though Malcolm Kane, Rook's head scientist, doesn't think they are up to the challenge.

During a demonstration, Blindstrike attacks Rook Unlimited forcing the Flex Fighters to defend the facility. Jake does some investigating and discovers that Blindstrike is in league with Rook's former partner and co-founder Dr. Racine Cleo (Dr. C for short) who was long thought to be dead. Meanwhile, Nathan and Ricardo begin having issues when the latter's jock like attitude gets on the former's nerves.

Villain Circuit-Stream plans to hack into Rook's satellite to release everyone's personal information. He gets help from the mysterious Stretch Monster who gives him a serum that gives him technopathic abilities and wrecks havoc across Charter City. The Flex Fighters in the meantime must also deal with their online presence when on the FlexFighterNet, users begin to rate the heroes causing Ricardo to have a huge ego and decides to live stream their current mission.

After a disastrous mission involving the Freak Sisters, Kane gives the Flex Fighters 48 hours to decide who should be the leader creating competition between them. Rook creates new robotic drones called stretchipedes to help out in various situations. The drones prove to be more useful than the heroes, but they soon become unstable and attack the Flex Fighters due to secretly being controlled by Stretch Monster.

"Smokestack" Jack Kinland is given smoke based powers by Stretch Monster and decides to start a turf war in Old Town, the original Charter City. The Flex Fighters are convinced by Rook to try and be more close with Kane, however Kane is revealed to have a past connected to Kinland and he finds himself brought back into the fray when his old gang, the Stickshifts, re-recruit him to help take down Kinland and his new army.

The Flex Fighters face a new threat in the form of Quick Charge, a villain with electricity powers. She is actually Dr. Sarah Kamen and blames Rook for knocking her out of the energy business and plots revenge by destroying his generators. Meanwhile, Jake attempts to ask out his crush Riya Dashti and Nathan and Ricardo discover that the former's grandfather knows that they are actually the Flex Fighters.

Jake feels guilty about not telling his father about his double life as Stretch. The Flex Fighters are once again pitted against Blindstrike who scans a map of the Pearl Islands, the known location where Dr. C's plane went down and where the formula for her Hyperflexarium is located. However, when Jake misses a parent-teacher conference, he is grounded forcing Nathan and Ricardo to do the mission alone.

While battling minor, misunderstood crooks Mortar and Brick, Jake is sprayed with an unknown substance that makes him lose control of his powers. Rook asks for a sample of the substance to be taken back so that he can make a cure. In the meantime, Jake has Ricardo pick up Riya for the dance and the two end up bonding over mutual interests. Nathan and Erika spend time together after the latter's date turns out to be narcissistic.

While on a school field trip at the Cleo Museum, a group of special op criminals called the Tech Men arrive to steal a valuable mineral called Prolotite. Jake, Ricardo and Nathan find themselves in a difficult situation of trying to save the students without revealing their identities. Eventually, the situation becomes more complicated with the arrival of Blindstrike, whom the Flex Fighters deduce is someone from the school, and Stretch Monster.

The Flex Fighters begin to investigate Blindstrike's identity and the possible location of Dr. C. They discover all the villains they've faced under Rook Unlimited and learn from Multi-Farious that they are unwillingly experimented on by Rook. The Flex Fighters track down Stretch Monster who claims to be in the unwilling employ of Dr. C and that he wants to be free of her. While Jake is willing to help their former enemy, Nathan and Ricardo are unsure of the alliance.

In flashback, Stretch Monster drains the brainwaves from a scientist. In the present, Stretch Monster back stabs the Flex Fighters. The team realize that they need to locate the Prolotite to stop him and figure out that Blindstrike's costume is full of Prolotite. After an exhausting battle, they manage to finally defeat and capture him. However, Stretch Monster arrives and kidnaps Blindstrike, forcing the Flex Fighters to chase down their nemesis.

The Flex Fighters must take down Stretch Monster for good and his Flexarium army. The team also must deal with the fact that Blindstrike is really Riya and that Dr. C has been trying to take down Rook as he is really Stretch Monster. With the Flex Fighters now considered criminals due to Rook's power, they have to decide what their next move is and how to go about with their status besmirched.