Jesse begins his new job at Misty Island Park. However, just as he meets Mr. Naugle, Randolph, and Marlene—the crew of the rescue center—he quickly becomes unpopular. His friend Willy, the orca, eats all the fish intended for the sick and injured animals. Shortly after, Jesse has a confrontation with Mr. Naugle, the center's director, and decides to quit his job abruptly. Then something extraordinary occurs: Jesse suddenly realizes that he can understand Willy, and the whale seems to understand him as well. Randolph, a Native American, explains to Jesse that there are children who can communicate with animals. Are Willy and Jesse soul brothers?
The parents of a baby dolphin have died because of barrels of toxic waste dumped in the sea. He is taken in at the station, and Marlene decides to name the clever little fellow Einstein. Einstein quickly wins everyone's hearts and soon becomes a full-fledged member of the Misty Island family. Meanwhile, Jesse and Willy are busy solving the case of the toxic waste dumps. They soon discover that the crooked Machine is behind it once again.
Rockland Stone, also known as Machine, has devised a particularly cruel scheme this time: he uses sonar to disorient the whales. The crew from Misty Island attempts to assist a stranded whale, but their efforts quickly become nearly impossible. Suddenly, Rockland Stone arrives and offers his help with the rescue operation. Everyone is excited about his offer—except for Willy, who suspects the true intentions behind Stone's facade as an environmentalist.
Annie is writing an article about environmental protection. She, along with Jesse and Marlene, has arranged to meet on Rockland Stone's new research vessel to gather more information. However, Jesse soon realizes that something is wrong on board. Why doesn’t Captain Frye want her there? Is the captain using the ship to dump toxic waste into the ocean?
Jesse and Willy's trip takes an unexpected turn when Jesse encounters a giant eel while exploring underwater caves. When the eel threatens him, Jesse attempts to communicate with it and discovers that its anger stems from the radioactive waste that has transformed this once ordinary eel into a monstrous creature. Jesse quickly informs his friends at the Oceanographic Institute about the situation.
Machine remains fixated on eliminating Willy. This time, it deploys a giant squid to attack him. However, the creature poses a threat not just to Willy but to all the animals at the Oceanographic Institute. Together, Jesse, Marlene, and Randolph work to ensure the animals' safety while strategizing to outsmart the enormous squid.
Lucille, the lovable seal, admires everything that humans do and tries to imitate them. When some unscrupulous characters come to the area and attempt to recruit her for a circus, she eagerly agrees. However, after a short time, Lucille realizes how awful it is to be a prisoner. She becomes even more delighted when Jesse and Willy arrive, promising to help her escape.
Misty Island is in turmoil: more and more sharks have been sighted recently, and they are even attacking people. Randolph, Marlene, and Jesse try to help, but only Jesse can truly make a difference. He manages to communicate with one of the sharks and discovers that Machine has stationed his submarine nearby. By attracting the sharks, he plans to drive the people out of the area so he can build his oil rigs without any disturbances. However, the unscrupulous villain hasn't accounted for Jesse and Willy.
Lucille, the seal, reaches out to Jesse for assistance because there is an issue in Pelican Bay. For a while now, the birds have been laying eggs with such thin shells that they break before the chicks can survive. Jesse speaks with the pelicans and learns that DDT is being stored nearby in an old cannery. This herbicide poses a serious threat to wildlife. In response, Jesse informs his friends at the Oceanographic Institute about the situation.
Machine's greatest ambition remains to destroy his arch-enemy, Willy. This time, he is targeting the salmon, which play a crucial role in Willy's diet. Fortunately, Marlene, who has been working for years to help protect the endangered salmon, notices the impending danger in time. Without hesitation, Machine begins cutting down the old-growth trees in a nature reserve to pollute the rivers.
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