The film revolves around a special team of trained secret agent animals, equipped with advanced tools that allows the mammalian members to talk to humans. The primary field team consists of Guinea pigs Darwin (team leader), Juarez (martial arts), and Blaster (weapons/transportation), star-nosed mole Speckles (cyber intelligence) and Mooch (Reconnaissance). The unit’s leader Ben, orders an unauthorised infiltration of the residence of home electronics and appliances magnate, Leonard Saber, the owner of Saberling Industries, who has been under FBI investigation. The team is able to retrieve sensitive information about a sinister scheme that is set to occur in 48 hours. However, when Ben’s superior Kip Killian arrives for his evaluation, his astonishment at the team’s capabilities and technology is overcome by his indignation at Ben’s unauthorized mission and the fact that the downloaded intelligence appears to be useless information about Saber’s coffee makers. As a result, the government agent orders the unit shut down, the equipment seized and the animals to be used as experimental subjects to be killed. With the help of their human compatriots, Darwin, Juarez, Blaster, Mooch and Speckles escape with hopes of stopping Saber’s scheme, but find themselves in a pet carrying case bound for a pet shop.
Trapped in the store’s pet rodent display case, G-Force meets Hurley, a laid-back guinea pig, Bucky, an irascible hamster, and three sycophantic mice. Although Blaster and Juarez manage to get themselves sold to a family with plans to return to extract their comrades, Speckles’ own attempt to escape by playing dead ends disastrously when he is thrown into and supposedly crushed in a garbage truck. Meanwhile, Mooch manages to return to Ben to tell him where his mammalian agents are, but Darwin escapes with Hurley before he can arrive to collect them.
While Blaster and Juarez escape their new owners to return to Ben, he and his assistant Marcie discover that the discredited intel has a destructive computer function that apparently hid the scheme. At this time, Darwin and Hurley make their own way to their superior. En route, Darwin sees a Saberling coffee maker and decides to investigate it, but his examination of the machine makes it come alive as a dangerous fighting robot that he and Hurley are able to defeat by making it run right into the path of an oncoming pickup truck. Later Darwin and Hurley transport the wreckage to Ben by a skateboard. However, upon arrival, Ben confesses the shattering information that they are not special genetically enhanced animals as previously told, but ordinary ones Ben took in and trained for the team; Juarez was a delicacy at a roadside tapas stand in Pyrenees, Blaster was found at a hair and cosmetics lab where a hair gel was being tested for allergic reactions, Speckles was found before his family and home were destroyed to build a golf course, during which he became blind and had to wear special glasses to help him see, and Darwin was adopted from the pet store after his parents abandoned him because he was the runt of the litter. However, Hurley lifts them from their despair by reminding the team of the astounding feats he has seen them do and the fact that they obviously made themselves extraordinary on their own.
Emboldened but with little time to stop the scheme, Ben provides the field team with the means to infiltrate the Saber residence and plant a virus in the computer mainframe. Unfortunately, FBI agents are ordered by Killian to capture the animals dead or alive, forcing the team to elude them with an extended pursuit thanks to a high speed vehicle especially designed for them called the Rapid Deployment Vehicle (dubbed the RDV by Darwin) and Mooch acting as their camera in the air. During the chase, one FBI SUV gets trapped by moving trucks, while another SUV crashes into a RV, and the last one gets caught in the middle of a fireworks display, though none of the agents are harmed. After the team infiltrates Saber’s mainframe, they encounter a bomb trap but they manage to avoid it because of their size. Meanwhile, Hurley notices a Saberling microwave oven, which transforms and attacks. In an appliance store, all of the machines also transform into killing machines and begin combining with each other. The microwave tries to kill the 3 guinea pigs but is destroyed by the bomb trap. The team takes on the monster, and the resulting battle separates the group, leaving only Darwin and Mooch to take the mainframe down. At the same time, Leonard Saber is shocked to discover that his appliances have become killing machines, expecting them to simply be able to effectively communicate with each other.
Meanwhile, Killian leads his men to take advantage of this obvious pretext to finally openly move against the industrialist thinking that he was the mastermind and interrogate him in the command truck. Ben and Marcie arrive at the scene and they watch Darwin trying to infiltrate the mainframe and shut it down. When Darwin reaches the mainframe, he finds out that Speckles, who actually faked his death and somehow obtained another pair of glasses after his original one was taken away earlier, is the mastermind of the plan. Speckles explains his masterstroke: to cause a massive planetwide bombardment of space junk pulled from orbit to make the planet surface uninhabitable, admitting that he snuck into Saber’s base and planted the control chips into the devices and used Sabersense as a cover for his plan, and that he was the one who sabotaged G-Force’s presentation to ensure that they didn’t find out about his sinister plot. He also explains that the reason behind his plot is because he wants revenge on the human race for the death of his family. Speckles promptly amalgamates the various appliances in the vicinity into a giant walking robot, which, combined with a localised bombardment of orbital debris, soon overpowers the police force and grabs the command truck, with Marcie, Killian, Saber, and Ben inside. During the fight, Speckles summons one of his robots to kill Darwin (who loses his parachute and the PDA in the process), but Darwin manages to persuade Speckles that his new family is with the rest of the team and Ben, who had taken them all in. Speckles concedes, and realizing that he has gone too far, tries to shut it down, but he has lost control and the machines continue their onslaught. Darwin uses the computer virus on his PDA (which was recovered by Mooch earlier) to take it down, destroying the robot and nearly killing Hurley while the FBI take Saber into custody to presumably find out information from him.
The guinea pigs are personally commended by the FBI Director who also appoints them special agents of the FBI. Furthermore, G-Force is reinstated as a unit of the Bureau and expanded with Hurley, Bucky and the mice inducted as new recruits. Meanwhile, Saber makes the largest product recall in history, Speckles is given the punitive duty of personally removing the malicious chips from all Saber products, which number into the tens of millions, and Agent Killian is relocated to an FBI base in the South Pole as a punishment for capturing G-Force.