After David and Amos are called to the discovery of $8,000 found at the local beach - an unusual discovery for such a quiet community. That same evening, Amos is murdered by an affiliate of local seafood magnate Walter Boyett when Amos reveals his suspicions of Boyett's operations. Scott is alerted to the crime the following morning, ultimately resulting in Scott hesitantly taking in Hooch, Amos' pet Dogue de Bordeaux. Scott immediately takes Hooch to the new town veterinarianEmily Carson. Scott pleads with Emily to take in Hooch as he has no experience of handling such an animal before. However, Emily insists that Hooch will be good for Scott, who lives alone.
Celebrating the approval to search Boyett Seafood, Scott treats Hooch but notices his refusal to eat - Scott considering this as a consequence of Amos' death, the long term owner and presumably, only companion to Hooch. Scott and Hooch are seen to establish a closer bond with each other. The next day, the police search Boyett Seafood but find no evidence of any illegal activity. With his transfer pending the following day, Scott is relieved of jurisdiction of the case and is given to David by Police Chief Howard Hyde. Frustrated with reaching a dead end in the case, Scott meets with Emily, leading the two to spend the night together. In an eurekamoment, Scott finally realises why the earlier search of Boyett Seafood turned up nothing - instead of searching for imports, Boyett Seafood was actually exporting goods. Armed with this new lead, Scott takes Hooch back to the factory to stake-out. The following morning, David arrives upon Scott's request with the earlier recovered $8,000 from the beach. On a hunch, Scott commands Hooch to trace the scent of the money to anything he can find within the factory, ultimately returning with the exact type of bag the wad was discovered in.
Scott travels to the Lazy Acres Motel, the false address that which Zack Gregory was listed as a tenant. Scott interrogates the Motel owner into revealing where Zack is, only to be held up at gunpoint by him moments later. Zack orders Scott into his car to drive away, but Scott crashes the Cadillac into a concrete barrier, propelling Zack through the windshield and pinning him down by the neck, provided assistance of Hooch. Scott interrogates Zack into revealing that he killed Amos, and also revealing that Walter Boyett is in on the illegal money trade going on at his factory, but is not in charge of it, to Scott's surprise. Scott returns with Hooch to the factory, and is unexpectedly joined by Chief Hyde. Already suspicious of Zack's earlier confession, Scott confronts Hyde, believing him to be in charge of the money laundering operation at the docks, using the gigantic ice cubes to cover the wads of cash being sent out of the country. A firefight soon occurs between Scott against Hyde and Boyett, with Hooch being able to ambush Boyett from above, although Boyett is able to shoot Hooch in the process. Confronting Hyde, Scott is initially coerced by the corrupt Police Chief to frame Boyett, who is subsequently killed by Hyde.