Plot

Stuart and Snowbell set out across town to rescue a friend.

Stuart's mother is being over-protective of him, especially when he narrowly escapes injury in a soccer game. His big brother George has also made a new friend, Will, so Stuart is feeing lonely. Stuart rescues a canary, Margalo, from a falcon; she moves in with the Littles. One day, Margalo is nowhere to be found, so Stuart and Snowbell set out across the city to find her while George covers for Stuart (the first time he's had to lie).—Jon Reeves <jreeves@imdb.com>

A young male mouse meets a new friend who is being controlled by a conning and vicious falcon. With the help of his family, he does his best to help his new friend gain freedom. Although, the falcon has other ideas for both of them. They work together to defeat the falcon.—RECB3

Two years after the first film, Stuart Little has settled into family life with his parents, older brother George, and baby sister Martha, who has yet to say her first words. Stuart is becoming tired of his adoptive mother Eleanor's over-protectiveness due to his small size and is finding himself lonely when George would rather play with his own friend, Will (Marc John Jefferies). Stuart is looking forward to a soccer match with George, but Eleanor is worried that Stuart might get crushed by any of the players in cleats.

Stuart is benched for most of the game, passing orange slices to players during the break. With 40 seconds left in the match, a player gets hurt, and Stuart is asked to take the field. Stuart Little (Michael J. Fox) questions his ability after a grueling soccer match alongside George (Jonathan Lipnicki), who kicked him with a soccer ball. Stuart is found by Frederick and Eleanor hanging on the back of the net.

Stuart becomes even more downhearted after George's toy airplane gets broken in an accident because of him. George and Stuart had built the model airplane together, but then George went to play PS2 with Will. Stuart decided to finish the plane himself, but accidentally ends up turning it on. Stuart is unable to control the plane, and it flies out of the house into a park, where it crashes. This prompts George to furiously throw it into a trash can

However, Stuart's dad Mr. Frederick Little (Hugh Laurie) tells him that for every Little, there is a "silver lining"- a good thing that comes out of an apparently bad situation. Stuart tries to make new friends at school, but everyone is busy with a lot going on in their lives.

When driving home from school in his roadster, Stuart saves a female canary named Margalo (Melanie Griffith) who is being pursued by a peregrine falcon (James Woods), and they become friends. But Margalo is secretly working with the Falcon to case and steal from households. When he presses her to find and take an object of value, or lose the sanctuary he promised her, Margalo can't seem to concentrate on her assignment, as she is beginning to have tender feelings for Stuart. Falcon eventually loses patience and threatens to kill Stuart if she doesn't deliver. Sadly, Margalo takes Mrs. Eleanor Little's (Geena Davis) diamond ring.

When the family sees the ring is missing, they think it has fallen down the sink. Stuart offers to be lowered down the drain on a string to get it, and nearly succeeds. When the string breaks Margalo saves him, and his thanks to her only make her feel even more guilty, so she decides to leave. When Stuart can't find her, he assumes she has been kidnapped - and that Falcon is somehow involved. He leaves on a quest to rescue her with the household's reluctant cat Snowbell (Nathan Lane), but not before setting up a plan with George. Stuart convinces George to conduct a series of elaborate (and extremely unconvincing) lies to Eleanor in order to cover for him.

Stuart and Snowbell decide to get information on Falcon's whereabouts, so they enlist the help of Monty (Steve Zahn), an alley cat, who tells them that Falcon's lair is at the disused observation deck of the nearby Pishkin Building and warns that he is an extremely dangerous foe. Stuart and Snowbell hatch a plan to use balloons to get Stuart to the top, where he finds out that Margalo is Falcon's slave, and was forced to take the ring. He tries to save her, but Falcon traps Margalo in a paint can, and drops him from an immense height to his presumed death. However, he lands on a soft trash bag in a garbage truck and is taken to a garbage barge out at sea.

In the meantime, Snowbell has also ventured up the Pishkin Building, and frees Margalo from the paint can, only to become trapped in it himself. Snowbell learns from Margalo that Falcon killed Stuart. Margalo breaks free from Falcon's control, and flies away with Eleanor's ring, prompting Falcon to give chase.

On a garbage scow where he has ended up, Stuart blames himself for everything and has almost lost all hope. But suddenly, he finds George's broken plane, fixes it up, and flies to save Margalo, who, having been freed by Snowbell, just fled from Falcon.

Meanwhile, George, after being reprimanded by his parents for his deception and interrogated on Stuart's true whereabouts, confesses where Stuart is to them, prompting them to head out and look for him. The Littles follow Stuart by taxi as he begins an aerial adventure through the park, with Margalo at his side. Eventually, they lose the Falcon, but he catches up and makes an attempt to kill Stuart, when he detaches the upper wing of the plane, damaging the main wing and causing it to enter a steep nosedive, which fails when Stuart recovers from the dive, nearly missing the Littles. Stuart then realizes he can't run from Falcon and lets Margalo off.

Stuart turns and flies the damaged plane in a kamikaze run while Falcon goes into an attack dive. Stuart uses Mrs. Little's ring to temporarily blind Falcon and jumps out using a Bandana as a parachute. The kamikaze attack works, and Falcon is struck head on and defeated. Although Falcon survives the attack, he falls out of the sky and lands in a garbage can that Monty is scavenging in, and is presumably eaten by the cat, but not before Stuart falls when his parachute is sliced apart by the propeller of the shattered plane, and then is rescued by Margalo.

Stuart is congratulated by his family, and Margalo, who gives Mrs. Little her ring back, and Snowbell reunite with them as well. That evening, Margalo leaves with the other birds to migrate south, but not before saying goodbye to her friends. Stuart says the "silver lining" is that she'll be back in the spring, and his baby sister, Martha (Anna and Ashley Hoelck) the infant daughter of the Little family, says her first words: "Bye-bye, birdie."