OSS agent Marissa Wilson (Jessica Alba) is attempting to capture a criminal named Tick Tock (Jeremy Piven), who purchases a mini-disk stolen from OSS. Despite being nine months pregnant, she continues her pursuit against the admonitions of her boss Danger D’Amo (also played by Jeremy Piven). Tick Tock is captured and the mini-disk, which contains information on a weapon of mass destruction called Project: Armageddon, is retrieved.
At the hospital, Marissa meets her spy-hunting TV host husband, Wilbur (Joel McHale), who thinks she is an interior decorator, and her two stepchildren by him, twins Rebecca (Rowan Blanchard) and Cecil (Mason Cook). Marissa gives birth to a daughter, Maria. Rebecca does not accept Marissa as a replacement for her deceased mother, and delights in playing pranks on her. Attempting to strengthen her rapport with Rebecca, Marissa gives her a red-sapphire necklace that she says her own parents gave her when she was Rebecca’s age.
The media reports that time is speeding up at an increasing rate. A criminal mastermind called the Time Keeper (also played by Piven) claims responsibility, saying he will unleash Project: Armageddon as punishment upon a society he believes wastes time with meaningless pursuits instead of treasuring time with one’s loved ones. The Time Keeper demands that Tick Tock bring him the Chronos Sapphire, which is revealed to be the jewel in the necklace Marissa gave Rebecca. The OSS calls Marissa out of retirement, and instructs her to bring the Chronos Sapphire with her. When Marissa asks for it from Rebecca, it further strains their relationship. When Marissa arrives at OSS headquarters, she discovers that the box Rebecca gave her did not contain the jewel, but it contained baby food.
Tick Tock’s henchmen break into Marissa’s house, and Rebecca and Cecil are directed to take refuge in a Panic Room, where they view a video of Marissa informing them of her secret career. The twins escape and go to OSS headquarters, where Marissa’s niece and their step-cousin, Carmen Cortez (Alexa Vega), gives the twins a tour of the defunct Spy Kids Division.
As Marissa pursues Tick Tock, Rebecca and Cecil go after the Time Keeper. Their search leads them to a clock shop, which is Tick Tock’s headquarters. The twins view a video of the Wells Experiment, which reveals the nature of the Chronos Sapphire in Rebecca’s necklace. The twins are captured by Tick Tock, but are rescued by Marissa and Carmen, though Tick Tock manages to steal the Sapphire. Wilbur’s investigations lead him to the clock shop, but he is shocked to learn that Marissa is a spy. When he destroys the footage that he and his cameraman filmed of the battle, he is fired, and becomes estranged from Marissa and the children.