Many years have passed since Stuart Little’s early adventures, and life in the Little household has become peaceful and comfortable. Now older and more confident, Stuart has grown into a clever young mouse who loves exploring the city in his upgraded model cars and aircraft. George, now a teenager, is busy with school and sports, which sometimes makes Stuart feel left behind. Even so, Stuart tries to stay positive, believing that another adventure will come when he least expects it.

One day, while flying his miniature plane through Central Park, Stuart spots a mysterious object crashing into the trees. After landing to investigate, he discovers a small metallic pod and a frightened mouse named Liora hiding inside it. She claims she has escaped from a group of high-tech thieves who have been experimenting on small animals to assist in their crimes. Stuart, remembering how Margalo once came into his life, convinces Liora to come home with him for safety.

The Littles welcome Liora warmly, though Snowbell remains suspicious of her dramatic arrival. As Stuart spends more time with her, he learns that the thieves are searching for a powerful micro-device capable of controlling small machines remotely. Worse yet, Liora believes the criminals have tracked her to New York. Despite the danger, Stuart promises to protect her, though he secretly fears he might not be brave enough for what lies ahead.

Their fears quickly become reality when the thieves begin leaving clues around the neighborhood and targeting the Littles’ home. To keep his family safe, Stuart teams up with Snowbell, George, and even his nervous friend Monty the cat. They uncover that the criminals plan to use the device to coordinate a massive citywide heist. Stuart realizes that only someone as small as himself can infiltrate their hideout unnoticed.

In a daring nighttime mission, Stuart pilots a new stealth glider built with George’s help. He sneaks into an abandoned warehouse where the thieves are preparing their operation. Using quick thinking, he manages to steal the device back, though he is spotted and chased through ventilation shafts and machinery. Just when he is cornered, Snowbell creates a chaotic distraction, allowing Stuart to escape with the device.

With the plan ruined and the police alerted, the thieves are captured, and Liora is finally safe. The Littles celebrate Stuart’s bravery, reminding him that being small has never stopped him from doing great things. As peace returns, Liora decides to stay in New York, and Stuart realizes that even as time changes, adventure will always find him—especially when he opens his heart to it.