Mastermind Emil Radick (Mel Ferrer) watches a motorboat from shore, talking to two men on the boat -- Carl Reed (Keith McConnell) and Larsen (Bucklind Beery). They test the current, then dump some debris overboard.
At the beach, surfer David Hammond (Bill Langenheim) argues with his girlfriend Cathy Doar (Pauly Gardner). As she leaves, David follows her, and Radick's two henchman grab him and take him away in a van. Another member of their party, Melissa Carter (Debi Parker), finds some junk on the ocean floor. McGarrett and the Navy arrive to investigate. They speculate that the debris recovered recently at this and several other locations is part of a Russian spy submarine which went down off Hawaii about a year before. About half of the submarine was recovered at that time. The Navy wants Five-O's co-operation to find the remaining parts and to keep the discovery under wraps. McGarrett is totally in agreement, though he is suspicious why all this debris suddenly washed up a year later.
One of Radick's goons enters the home of Doctor Margaret Hammond (Laura Campbell). He phones his boss who transfers the phone to her kidnapped brother, who tells Margaret that he fears for his life. Since Margaret is the chief oceanographer working on a secret U.S. government project, Radick wants her to use her access to get to a restricted area of the beach near the government research facility.
Margaret arrives by car at the government dock with a box of more debris. She takes a boat out into the ocean where she dumps the stuff overboard.
Radick arrives at the abandoned Malalo Mission School where David is being held prisoner. He takes David's dog tags.
Dr. Hammond is talking to McGarrett about the recovered parts just as Dr. Grant Ormsbee arrives. Ormsbee describes one of the parts as a "computer discharge mechanism" which he can use it to extract information from the sub's computer that he has had for almost a year. McGarrett wonders if all the original information accumulated from the submarine during its tour of duty is still intact. Ormsbee asks for Dr. Hammond to be assigned to his own unit because of her familiarity with local current patterns and requests that the area be searched for more debris.
As she arrives home, Radick's punks grab Dr. Hammond and bring her, blindfolded, to the school, where they grill her about her connection with Ormsbee. Radick says "you will help him [Ormsbee], as I direct." He shows her David's dog tags and threatens David with "extreme pain or loss." She warns Radick about McGarrett. Radick says that if McGarrett gets too suspicious, they will kill him.
Williams talks to his friend Captain Pete Morelli (Bob Turnbull) about diving in specific locations to see if more debris can be uncovered.
David's girlfriend Cathy visits Margaret and mentions the fight they had, saying David hasn't returned to their apartment. Margaret tries to avoid talking to Cathy, saying that she can't help.
McGarrett arrives at the government research station where Ormsbee is testing equipment. Their discussion ends up in a squabble over the search for more units. Ormsbee refuses to give McGarrett any more time for searching.
Cathy visits HPD headquarters, where she files a missing persons report on David with Sergeant Mirataki (Tommy Fujiwara). He says no one has been found matching David's description, suggesting that David is "cooling off" after their fight.
Danno and Chin talk to some surfers who found a new piece of electronic gear.
One of Radick's goons tells him that Cathy has been asking questions about David. Radick tells him to take care of her.
At the research station, Ormsbee says that the most recently discovered part fits the computer "like a glove." McGarrett is not satisfied, saying it's too neat and convenient that this key device turns up just when it is needed. He wonders if the disengage unit might erase all the contents of the computer's memory bank instead of extracting them. Ormsbee says that he will test the device thoroughly first.
At the beach, one of Radick's punks talks to Cathy, who says that David has gotten "his head together" and will meet her at Makapuu Lookout. She phones Murataki and tells him that everything is now OK. As Cathy waits by the side of the road, the punks run her over!
Cathy's body is removed. The cop on the scene considers it a hit and run.
Captain Morelli says that Danno has "second sight" since a lot of debris was found along with a U.S. government work tarp in the area Danno suggested.
Chin Ho brings the report of Cathy's death to HPD headquarters, where Mirataki reads it. He wonders if Hammond is still considered a "missing person" since the person who reported him is now dead.
McGarrett visits Dr. Hammond, wondering how did the unit get through the rocks without damage. She says that "ocean currents can be very unpredictable." He wonders why she seems so "up tight" because of his questioning.
Ormsbee tells McGarrett to stay away from his investigation. McGarrett pleads with Ormsbee to postpone connecting the disengage unit to the computer bank, but Ormsbee says that if he waits, the computer data may deteriorate. McGarrett threatens to go to the Chief of Naval Intelligence. Ormsbee says he already did that, and now has total authority over the project. The test will be in three hours.
In the Five-O office, Chin Ho mentions the fact that David Hammond is missing. McGarrett wonders why his sister Margaret never mentioned this.
Margaret is grilled again by Radick and his men as to when Ormsbee will complete his testing. When she asks why are they seemingly helping Ormsbee to recover the data, Radick says she should "consider the art of indirection." He says, "I think of myself as an ecologist dealing in the balance of fear, greed, desire." He insists that Ormsbee commence the test and threatens David with "a more painful interview."
The punks take Margaret home. One of them sneaks into her yard behind her as she meets McGarrett, who let himself in. After she sees the tarp recovered with the debris, Margaret finally breaks down and tells McGarrett that David has been kidnapped. The two of them try to determine where in the city the hideout is located based on time, sounds and other information. Radick's two punks attempt to assassinate McGarrett, and a gun battle ensues. McGarrett wounds one of them, and they make their getaway.
Five-O arrives at Margaret's and Duke with her help is able to pinpoint the building where David is being held captive. McGarrett phones Ormsbee and, after mentioning details of the kidnapping, finally convinces him to stop testing the discharge unit, saying that it is a fake, designed to wipe the computer's memory bank clean. Shortly after at the research facility, Ormsbee demonstrates that this is indeed the case.
McGarrett arrives at the mission school with Five-O and HPD, but Ormsbee drives up and goes into the building first. Encountering Radick, Ormsbee suggests that the jig is up, and that Radick and his men should flee as quickly as possible. Five-O breaks in and arrests the two punks, but Radick escapes. His flight is short-lived, as McGarrett flattens the tires on his car.
McGarrett lambastes Ormsbee for his "blatant stupidity" and books him for "interfering with a police action."