See Spot Run(2001)

SHORT VERSION:
Murdoch and the FBI eventually find out that Spot is living with Gordon and James, and they take him back to the canine training facility. However, the time Spot has spent being a normal dog with Gordon and James has irreversibly changed him, so he soon escapes the facility to rejoin them. After finding out about his escape, a fuming Murdoch tells his staff that he is heading back to Gordon’s apartment to get him because he knows that that is where he has run off to. Gino and Arliss, who were just about to infiltrate the facility to find and kill Spot, overhear this, and already knowing where Gordon lives, they make their own way back there.

Gino and Arliss find Gordon and James along the way to the apartment and chase after them, but Gordon and James manage to lose them. They return to the apartment so Gordon can call the FBI, but a gun-toting Sonny shows up with a tied-up Murdoch and makes everyone sit down, intending to wait for Spot to show up so he can kill him personally. Gino and Arliss then enter, and as Sonny chews them out over their failure to carry out the hit on Spot, Spot suddenly appears. When all is said and done, Spot subdues Sonny and bites off his other testicle, Gino and Arliss are also subdued, and the FBI shows up and arrests the mafiosos. Afterwards, Spot decides to stay with Gordon and James, but before Murdoch leaves, he gives Murdoch a few goodbye licks for being a caring handler. Stephanie then returns home from her business trip, and after finding out that Gordon and James took down a mob boss and his henchmen, she takes James back to her apartment and warns Gordon to not get within fifty feet of him or else she will call the police on him, thinking him to be a threat to her son’s safety.

A few days later, Gordon and Spot are at the park when Spot notices James and Stephanie nearby getting ice cream from a vendor, so he runs up to them and snatches Stephanie’s purse, then runs back to Gordon so she and James will come after him. Stephanie has a chat with Gordon, telling him that James told her all about what happened with the mobsters and that she also got confirmation on Spot’s now-former status as an FBI agent, and she thanks Gordon for saving James’ life. She then tells him that she is willing to give the possibility of them dating another shot, and Gordon replies that he is all for it, so long as James and Spot are included, and she agrees with a smile. She, Gordon, and James then walk off to play with Spot.

LONG VERSION:
While Agent 11/Spot is under the care of Gordon (David Arquette) and James (Angus T. Jones), he learns how to behave more like a normal dog and even engages in playful activities, something that Murdoch (Michael Clarke Duncan) told him never to do back when he was a puppy. However, while James and Gordon are at Petcetera with Spot getting a new toy for him, they come under attack from Sonny’s (Paul Sorvino) henchmen Gino (Joe Viterelli) and Arliss (Steve Schirripa), who are looking to cash in on a contract that Sonny put out on Spot. Gordon, James, and Spot are able to outwit the goons and escape the store, and they go to the police station afterwards to file a report about it, but they get directed to the obnoxious Ricky (Kavan Smith) (who, like Gordon, is trying to win the hand of James’ mother Stephanie [Leslie Bibb]). Ricky finds their story about mobsters trying to assassinate their dog to be laughable, so Gordon and James leave.

Later on, Gino and Arliss get a call from one of Gordon’s neighbors, who is responding to one of the false Lost Dog advertisements that they put up with a picture of Spot on it in an attempt to have someone bring the dog to them, and she tells them that Gordon has their dog before providing them with his address. While Murdoch and fellow agent Cassavettes (Kim Hawthorne) are down at the police station talking to a senior officer about finding Spot, Ricky overhears this and – within earshot of Murdoch – comments to another officer about how he doesn’t understand all of the fuss concerning dogs today, then brings up how Gordon and James earlier reported to him that the mafia had put a contract out on their dog. Immediately realizing that Ricky is talking about Spot, Murdoch walks right up to him and demands for him to tell him everything.

That night, Gino and Arliss arrive at Gordon’s apartment building, but before they can go in, Murdoch, Cassavettes, and a bunch of other FBI agents suddenly appear. However, they ignore the duo and head straight into the building, and knowing that they won’t be able to get to Spot with the FBI around, the mobsters quickly run off. Murdoch and Cassavettes have a chat with Gordon and James, and the latter shows Gordon pictures of Sonny, Gino, and Arliss before asking if he has seen any of these men, and Gordon informs her that the latter two tried to kill Spot while they were at Petcetera. Murdoch tells them that they shouldn’t be bothered by these men any longer now that Spot is going to be returning to the FBI, then he starts to take Spot away. Gordon and James protest this, but after Murdoch sternly tells them that Spot is U.S. government property, Gordon has no choice but to concede. Murdoch puts a shock collar on Spot and takes him out the door with him, though Spot puts up some resistance after James begs for him to not go. Both James and Spot fall into a depression and refuse to eat, and James eventually demands for Gordon to do something to get Spot back, but out of being upset himself, Gordon yells at him that Spot was never their dog and that he is just being an irrational kid, so James stomps on his foot and then shuts himself in Gordon’s bedroom. Stephanie then calls to check up on her son as she is making what has turned out to be a terrible journey back home from her business trip, but Gordon snaps at her, too, demanding to know when she will be here to get James. He then tells her that he will not let her treat him like an irresponsible idiot and calls her the irresponsible one, and adds that he is not a dog person and he doesn’t need a kid in his life, either. However, he is completely unaware that James has listened in on all of this.

Meanwhile, after watching a family play with their dog from his kennel in the canine training facility, Spot resolves to go back to Gordon and James, and he makes his escape after he tricks an agent into opening the kennel’s door. While Gordon’s attention is elsewhere, James sneaks out of the apartment and walks the streets hoping to locate Spot, and when Gordon finally does notice that he is missing, he heads out in his mail truck to find him. As this happens, Gino and Arliss prepare to infiltrate the canine facility in another attempt to get at Spot, but before they can even enter the main gate, a fuming Murdoch suddenly steps out. After chewing out his staff for letting Spot get away, Murdoch tells them that he is going to pay Gordon and James a visit because he knows that Spot has run off to rejoin them. Gino and Arliss immediately return to their car and head for the apartment building.

Gordon finds James walking near a children’s baseball field and get to talking with him, and he admits to the boy that he misses Spot and also apologizes for his outbursts against him and Stephanie, and he tells him that he was glad that he came to stay with him. As they share a hug, they are spotted from afar by Gino and Arliss, and Gordon soon takes notice of them and quickly puts James into his truck. After a vehicle chase followed by a chase on foot, during which Gordon subjects Arliss to the wrath of a vicious beagle on Bleeker Street that he has dealt with multiple times himself, Gordon and James manage to escape the mobsters. They run all the way to Gordon’s apartment, but when Gordon tries to call the FBI, a gun-toting Sonny suddenly enters with a tied-up Murdoch and forces everyone to sit down. He demands to know where Spot is, and after Gordon replies that he thought he was with the FBI, Murdoch informs him that he escaped to go be with them. Sonny thus tells them that they are all going to wait for the dog to appear, having plans to do away with him personally. Soon after, Gino and Arliss show up with the beagle still gnawing on Arliss’ coat, and Sonny grabs the beagle and tosses it out the living room window.

As Sonny criticizes his underlings for their inability to carry out the hit on Spot, Gordon sees the dog lying in wait inside his bedroom. Spot gets Sonny’s attention moments later, but when Sonny tries to shoot him, Spot bites his arm and makes the gun fly out of his hand and land near Arliss. Murdoch tells Spot to get the weapon, and Arliss hands the gun over to Gino to avoid being attacked before Gino, in turn, throws it back to Sonny. Thankfully, before Sonny can make any use of it, Gordon notices that he has pulled off Spot’s shock collar and is still holding it, so he switches it on with his TV remote and gives Sonny a good zapping. After Sonny drops the collar and the gun, Spot leaps at him and clamps his jaws down on his crotch while also sending both of them flying out the living room window and onto the ground, causing Sonny to lose his other testicle to him. Gordon then knocks out Gino, and Arliss gets attacked by the beagle again as he tries to make his escape. The FBI shows up and places the mafiosos under arrest, and Sonny is later shown in prison speaking in a falsetto voice and with ball bearings for testicles that clack together when he walks.

After the dust has settled, Murdoch calls for Spot to come with him, but Gordon tells Murdoch that Spot is staying with him and James. He explains that Spot just wants to be a happy, regular dog and be with people who care about him, and there is no way that he is going to let Murdoch take that chance away from him. He then decides to put Spot between himself and Murdoch in order to let the dog decide who he wants to stay with, and with little thought, Spot walks over to Gordon and James. The saddened Murdoch soon starts to leave, but Spot stops him and gives him a few goodbye licks for being a caring handler. Stephanie then finally shows up at the apartment building and sees the FBI agents all over the place, so she asks Gordon’s friend Benny (Anthony Anderson) what happened, and he tells her that Gordon and James took down a mob boss and his henchmen. Alarmed, she rushes into Gordon’s apartment to get some answers, and after James greets her, he tells her about the day he and Gordon just had. Interpreting Gordon as a threat to James’ safety, she warns him that she will call the police on him if he gets within fifty feet of her son, then takes her son back to her apartment. Spot tries to follow after James, but Stephanie forces him to remain with Gordon.

One day, Gordon brings Spot down to the park, and Spot notices that Stephanie and James are nearby getting ice cream from a vendor. He runs up to them and snatches Stephanie’s purse, then runs back to Gordon so they will chase after him. Gordon and James happily greet each other before Gordon has a chat with Stephanie, who informs him that James gave her the whole story about how he and Spot saved him from the mobsters, and she also checked out Spot’s background to get confirmation on his now-former status as an FBI agent. She gives Gordon her sincerest thanks for saving her son’s life, then says that she may have jumped to conclusions about him and is willing to give the possibility of them dating another shot. Gordon replies that he is all for that, so long as James and Spot are included, and she agrees with a smile. They and James then walk off to play with Spot.