While diving at a new aquarium research facility, Jonah and Nicole discover barrels dumped into the water. One of them is leaking and an unknown substance gets into Jonah's eyes, causing painful burns. Jonah is rushed to hospital and while Dr. Kelsay works to save his eyesight, Grant sets out to apprehend whoever has been dumping toxic waste into the sea.
George sends Grant to Abbot Bay to investigate sightings of a "monster" that the locals have affectionately called Abby. Meanwhile TV host Graham Sanderson schemes to undermine Grants efforts and claim all the credit for the monster's "discovery."
Jonah's friend Dennis is about to perform a potlatch dance in honour of Chief David. Dennis receives a gift from his uncle Charlie which is a replica of a thunder bird mask on display at the aquarium. Dennis and Jonah decide that the appropriate gift for chief David would be the original mask that once belonged to his people. The boys switch masks at the aquarium, but when they present Chief David with the original mask, they are surprised at his reaction.
Grant and his colleague Doug are investigating why a certain lake is highly acidic while another just a few miles away is perfectly healthy. They embark on a field trip accompanied by Jonah and Doug's Little Brother Billy, who lost his hearing in a white water accident. Grant and Jonah are in a raft when a mooring breaks and they become trapped in rapids. With Doug bound to a wheelchair, Billy, still traumatized by white water, is the only one in a position to mount a rescue of Grant and Jonah.
J.L is flying Grant and George back from a fossil hunting expedition. The plane develops mechanical trouble and J.L. is forced to make an emergency landing on a remote lake. J.L is unhurt but Grant breaks his arm and George gets a nasty bump on the head. The plane's radio is out, but J.L. deploys the Emergency Location Transponder (ELT). The excellent ability and professionalism of the Sartechs (Search and Rescue Technicians) is now showcased.
Nicole and Jonah train to enter the world famous Bathtub Race from Nanaimo to Vancover across the Strait of Georgia. With the aquarium facing a financial crunch, George talks Grant and J.L. into entering to attract sponsors. Just before the race, Grant and J.L discover that their feelings for one another have gone beyond that of just friends.
While JL and Nicole are searching for bullfrogs in Finn's Slough, a coral snake attacks JL but can't bite through her hip waders. At the aquarium Grant learns from Donna's friend Dr. Gupta that a boy playing in Finn's Slough was bitten by a snake and is now in critical condition. Grant captures the snake and while trying to milk its venom, Donna gets bitten. To treat the victims Dr. Gupta needs to know the exact species of the snake. Grant seeks help from the snake's keeper, reluctant recluse Charlie Dobbins.
A BC Hydro crew finds an intact fossil of a fish with legs. When Grant learns of the discovery he thinks the animal could be the "missing link" in the evolutionary chain. Grant takes Jonah and his friend Martin on a trip to study the fossil. Martin's father Don is a famous biologist who also joins the crew. The expedition proves to be an opportunity to study the distant past and for an estranged father and son (Don and Martin) to renew their relationship.
Driven by hunger, a wild cougar descends on Danger Bay, frightening the residents. Grant, Donna, Jonah and Nicole work with wildlife authorities to trap and move the animal while local hunters armed to the teeth are intent on destroying it.