The team has just captured their latest bad guy after a high-speed chase through a prehistoric theme park, complete with animatronic dinosaurs. But when they call Uncle Zachary to let him know, he's not at his desk and there's a distress signal. Dan, Tess, and Daisy make their first visit ever to Pole Position headquarters in San Francisco to check it out. There they find a trail of mysterious puzzle pieces and a business card for an Alfred McGuffin. When they call him, McGuffin informs the kids that Dr. Zachary hasn't been himself lately and was talking about "finding the colored fish".
On a hunch, the kids check some local restaurants with promising names, but quickly learn that someone has sent a videotape of them poking around Uncle Zach's office to the police, and that they are now wanted in connection with his disappearance. A policeman at Fisherman's Wharf recognizes them from the TV news bulletin, forcing them to flee, and they narrowly dodge a couple of FBI agents who were tipped off about their arrival in Chinatown. Tess suspects Alfred McGuffin, but Dan is convinced he's an honest businessman. Desperate for clues, Dan and Tess send Daisy back into PPHQ (since there are now police watching the building for the two of them). She and Kuma discover a secret recording in which Uncle Zachary was threatened by McGuffin, but Zach addresses him as Blake O'Connors. In the elevator, Kuma also finds a Chinese puzzle box hidden by Uncle Zach, containing a rock.
Wheels informs them that O'Connors / McGuffin was an international spy who served time at Alcatraz, and they put Uncle Zach's clues together. Using Roadie and Wheels to break into the prison, they find Uncle Zachary... in a wheelchair, paralyzed from the waist down! He explains to Dan that this is "why you and Tess have acted as my legs". Uncle Zach has one last puzzle piece, containing microfilm evidence that McGuffin and O'Connors are the same person. Before they can do anything, McGuffin, who is holding Uncle Zach prisoner, snatches it. The kids chase after him, hydrofoiling back across San Francisco Bay and dodging passing ships. McGuffin is captured, and all is well back at PPHQ... except how is Daisy going to get out of those Chinese finger traps?