Fifteen years after their original shipwreck on the S.S. Minnow, the seven castaways still live on the island, their days marked by small adventures and hopeful routines. In a parallel thread, a Soviet-style regime’s military scientists shoot down an orbiting satellite carrying a top-secret disc, which somehow survives the crash and lands near the group. The Professor, [Russell Johnson], realizes the disc’s alloy could be used to craft a new barometer, a tool that might give them warning about storms. With this discovery, he demonstrates that a massive storm is on the way and that a tsunami could erase the island if they don’t act. To survive and perhaps compel a rescue, the castaways band together to build a raft by tying their huts into a floating shelter.
The next morning, the castaways awaken to a startling turn of events: the raft has swept them away from the island. When Gilligan, [Bob Denver], accidentally sets the raft on fire, the smoke draws attention, and the United States Coast Guard spots them and rescues them from the open sea. Back in modern society, they grapple with a world that feels foreign—new technologies, fashions, and a level of media attention they could never have imagined. After a period of intense public fascination, the group gathers again for a Christmas reunion aboard the S.S. Minnow II.
Meanwhile, foreign spies uncover that Gilligan still holds the lost disc and begin a renewed hunt to recover it. The insurance company refuses to issue a settlement for the first Minnow unless all the surviving passengers sign a sworn statement absolving the Skipper, [Alan Hale Jr.], of responsibility for the wreck. The Skipper and Gilligan set out to secure those signatures, visiting their old companions one by one. First, they meet Ginger Grant, [Judith Baldwin], who is busy with a film career and notes how much the movie industry has changed since their days on the island; she agrees to sign. The Professor, having become a well-known figure whose fame threatens to overshadow his research, also signs after considering the tradeoffs between recognition and science.
Next, the duo heads to the Howells. Thurston Howell III, [Jim Backus], and Lovey Wentworth Howell, [Natalie Schafer], receive them with their characteristic elegance and wit. They host the visitors but also endure some sharp remarks from so-called friends who disparage Gilligan and the Skipper, prompting the Howells to help them leave. The spies, concealed among the guests, are eventually identified and removed along with the disparagers.
Their next stop is Mary Ann Summers, [Dawn Wells], who is about to marry her old fiancé, Herbert. She no longer loves him but feels bound by obligation to the ceremony. To spare Mary Ann from an unhappy union, Skipper and Gilligan deliberately disrupt the wedding where foreign agents are among the guests. In that moment, Mary Ann realizes that Herbert loves someone else and, relieved, agrees to sign the insurance statement.
With all the signatures gathered, the insurance company pays for the first Minnow and the former castaways celebrate a reunion cruise aboard the Minnow II. The spies mount one last attempt to seize the disc, but the FBI intervene and secure the disc from Gilligan. The cruise proceeds, yet a storm erupts and the Minnow II is battered by the seas. In a critical misstep, Gilligan removes the magnet from the compass while cleaning it, sending the Skipper off course and steering the ship toward danger. The ship finally runs aground on a beach, and the passengers realize they have returned to their old island, discovering a fragment of wood from the original Minnow as a tangible reminder of their enduring bond.