McGarrett arrives on the scene at an "isolated reservation" after a local farmer claims three of his cows "were killed by some kind of biological experiment". Danno called him there after seeing the cows for himself: it's ugly. All three are petrified, as in "as hard as a rock". No insects want any part of the cows, there are "no flies" and "even the bugs are detouring". The farmer is beside himself, chattering to the HPD Officer (Bernard Ching) in Chinese. Assuring the farmer the state will pay for his cows, McGarrett then orders a "quarantine [of] this area, then get a refrigerated truck out here ... Then call the county morgue, tell Doc (Ted Thorpe) to standby".
Upon arriving at the morgue, McGarrett and Danno are introduced to Dr. Hewitt (Fred Titcomb), a veterinarian, and Dr. Funakoshi, communicable diseases, who are helping with the pathology. The bottom line: they don't now what they're dealing with. They have been able to eliminate just about everything in existence. It is "a bacteria that's completely unknown to us". Just as Doc is about to give it straight, Lieutenant Valed from Colonel Sindell's (H.M. Wyant) office shows up demanding the cows be returned to the Army. McGarrett doesn't budge, but rather leaves to go see the Colonel himself.
McGarrett discusses the situation with Sindell, still not budging off his jurisdiction. Sindell believes the investigation belongs in the prevue of the Army, while McGarrett implies cover-up such as seen in previous cases. Sindell claims he's not trying to cover-up anything but rather the Army had nothing to do with the cows being killed.
Jonathan Kaye (Joseph Sirola) arrives from Washington D.C. with Dr. A.L. Benjamin (Dana Elcar) in tow. After McGarrett describes what the cows were like, Kay and Benjamin brief about what is really going on: Dr. Alexander Kline (Ed Flanders) was brought in to perfect and develop what is known as a 'Q Strain.' All the Army had to do was put it into an aerosol and it can potentially wipe out all life on the planet. McGarrett sums it up best, "you people frighten me". Kaye calls it, "Necessary deterrent power".
While the briefing is taking place, Kline meets a woman (Loretta Swit) on a rocky beach and they become acquainted through small talk. She's a telephone operator and can pick up accents from different areas.
According to Dr. Benjamin, the entire project "seemed jinxed" with accidents and mistakes piling up. After thorough security checks and psychiatric tests, it turns out Kline was subconsciously sabotaging his own project and heading toward "a possibly irreparable psychotic breakdown". On the beach, Kline becomes philosophical staring into a tidal pool knowing life is everywhere and he has the means to wipe it out. Because of the immense pressures, Kline went missing and had been missing a year before the three dead cows. The mission is to find him and stop him due to the destruction he possesses.
Five-O sets out with HPD to find Kline. Chin hands out fliers to a group of officers in McGarrett's office. McGarrett wants surveillance only until a positive identification can be made and he will personally handle it from there. After the officers file out, Danno walks in with a list of private labs they'll hit up. Kline is continuing his experiments and needs a well-equipped place to do it.
Kline has taken a job at a lab where the head (Yankee Chang) notices 'Arnold' isn't looking well. After packing the test tube with 'Q Strain' into a case, Kline calls the operator and gets his friend from the beach! This is after trying to reach a phone number that continues to ring busy. When she asks for the name of the party, she finally recognizes his voice. Kline hangs up but she's left with information to track him down.
Kline goes to visit Abel Morgan (Karl Swenson) who is blind but figures out everything by feel. He's a woodworker and scrimshaw artist. Kline sounds depressed and feels there's no one else he can turn to. Just when it seems darkest, the telephone operator walks in, admitting she figured out where he was based on the information he left her to place the call. Leaving, Kline walks outside near collapse. The operator follows him, insisting on taking him to her place because he's obviously not well.
McGarrett and Danno check out the lab where Kline has been working. Dr. Soong is the man in charge and called Five-O upon seeing Kline's picture. Dr. Soong says the man's name is 'Arnold Clay' and has been working there "about five months". Danno checks on the home address while McGarrett calls "some experts down here to go over what he left behind".
Kline is delirious at the girl's apartment. She opens his case looking at various bottles of who-knows-what. She finds the metal cylinder holding the 'Q Strain' test tube. She opens it, removing the test tube and placing the pieces on the table.
Danno and Kono follow up on Kline's home address; a vacant lot and the neighbors have never seen him.
Kline comes out of his delirium realizing he's at the girl's apartment. He admits he's "a research technician". They introduce themselves, he is still using 'Arnold Clay' and she's Wanda Russell. She leaves for work to relieve a lady to pick up her dog and Kline contemplates his next move.
At the research facility, Five-O and the lab with Dr. Benjamin's help go over everything but no 'Q Strain'. McGarrett notices a unique scrimshaw piece and sets Chin to find out who makes them.
Wanda returns to an empty apartment while McGarrett talks to Abel. Abel tells McGarrett Kline is dying and "he's searching for peace in the certainty of death".
Wanda calls the research facility looking for Kline. Dr. Soong hands the phone to Danno who proceeds to scare the crap out of Wanda making her hang up. This after she tells him she doesn't know where Kline is.
Wanda goes to the one place she hopes to find Kline, the beach where they met. She's successful in finding him but Kline accidently shoves her into the water from the cliffs. He dives in saving her from drowning.
McGarrett and Danno question the operators at the telephone company in the presence of their supervisor (Elizabeth Smith). One operator gets their attention, Shirley Harris (Lynne Ellen Hollinger). Shirley is Wanda's best friend and tells them "Wanda's the kind who's always picking up strays". Shirley goes on to tell them he's probably at her apartment at "2466 Waimea Drive". McGarrett and Danno run out.
While Kline drives Wanda to the hospital, McGarrett and Danno check out her apartment. Kono runs in briefing on a radio call that a man fitting Kline's description just brought a woman to a hospital. They all run out heading toward the hospital.
The doctor's prognosis for Wanda is good. Kline visits her, apologizing for hurting her and telling her a little about himself, specifically his lonely childhood. He warns her to get off Oahu as soon as she can because everything on the island will be dead or dying "within the next 12 hours".
As Kline is warning Wanda, Five-O arrives ready to apprehend Kline. When he leaves Wanda's room, Kline staggers in the hall. When the young doctor from before tries to help, Kline shoves him into a door. Just then McGarrett and Danno round the corner and the chase ensues. It's short-lived as Kline falls next to a tree. McGarrett frisks him but no luck. Kline says, "It's hidden out there somewhere. You'll never find it in time".
Kline is admitted into the hospital under police guard. In his room, Jonathan Kaye, Dr. Benjamin and Colonel Sindell try various negotiation tactics to get Kline to tell them where the vial is. Kline won't budge, determined to see his "shock therapy" to the very end. Sindell goes off screaming at Kline about how his wife can't be moved.
This just shows scenes from Part One. No new scenes or information.
Picking up where Part 1 ended, except McGarrett rushes into Kline's room to pull Sindell off Kline. Sending the colonel outside, McGarrett, Kaye and Dr. Benjamin are left to talk Kline out of his plan. Kline believes his plan will stop germ warfare but McGarrett points out Kline can't stop the military from their experiments overnight and killing 750,000 people certainly won't. When their tactics fail, Kaye and Benjamin leave. McGarrett is the last to leave and Kline asks about Wanda, giving McGarrett a clue to help prevent disaster.
Jonathan suggests bringing in Dr. Malden (Ken Drake) and gets clearance to do so after talking to the President. Now it's a waiting game as Dr. Malden in not yet in Hawaii but should be arriving within 30 minutes. Sindell wants that half-hour alone with Kline but both the governor and Kaye shoot him down.
At Five-O, Danno has been talking to Wanda who showed them where she fell into the water. Five-O isn't the only ones asking her questions, "eight generals" also asked. Wanda just wants to know what's happening. McGarrett explains it to her: Kline created the germ and plans to wipe out life in Hawaii in order to save the world. "He asked about you. He cares about you very much". McGarrett feels they can persuade Kline with her help.
Wanda visits Kline in the hospital. It doesn't go as planned on either side, Wanda freezes and Kline screams at her leaving both in distress. It's not going to get better for Kline either as Dr. Malden is on his way. Walking into Kline's room, they drug him then Malden gets to work. Kline calls Malden, "the great mind bender". Malden's methods are no less than torturous and they don't work. The only bit of information is that "he had hidden the vial under a pier somewhere". They're back at the same spot: not knowing where the vial is. Malden debriefs the group, saying the more pressure on Kline, the more he resists. After sending Danno to check some areas, McGarrett suggests they release Kline. His reasoning: because Kline is on the verge of breaking down perhaps if he's allowed some movement he'll lead them to the vial or better yet, "come to his senses". Kaye deems it too risky but puts the responsibility of failure on McGarrett if they lose him.
Five-O tails Kline all over Honolulu, starting at Hotel Street. Eventually, he leads them back to Abel Morgan's shop. Kline and Abel have a deep conversation about love: "we're shaped by the things that we love". Abel sends Kline on his way, petting his dog the whole time. McGarrett and Danno pick up the tailing as Kono is sent inside the shop to see if the vial is in there. Kline's next stop is Wanda's apartment. He's not sure why he stopped there except to make sure she was leaving. All the airlines are booked so she's taking a friend's boyfriend's boat. She still doesn't understand why he's "going to murder people, thousands of people". Kline uses the analogy of a beehive: by his logic, he is saving the hive.
McGarrett and Danno continue following them to the marina. Kono reports no vials found at Morgan's shop. At the marina, Kline helps Wanda unload her car but gets into a fight with one of the guys there. McGarrett and Danno intercede, stopping the fight. The realization hits Kline that what he's trying to do is futile, especially after Wanda tells him she loves him. Kline agrees to take them to the vial.
McGarrett, Danno, Kline and Wanda head to the pier "located about two miles from Hawaii Kai Road at Coral Cove". McGarrett orders decontamination units and truck full of bleach. Kline walks out to the hiding spot, only there is no vial!
Chin and Kono show up followed closely by Kay and Benjamin and the Army decontamination unit. McGarrett suspects someone has taken it because high tide isn't that far this particular pier. Kline developed the timetable on his calculations based on the bacteria's rate of growth. They have five hours left before the vial begins to leak. "Now, if the combination of bleach and DS2 won't kill it, fire and steam will". Kaye makes it clear to McGarrett he doesn't want the 'Q Strain' destroyed to which McGarrett retorts, "I'm not gonna risk their lives to save your defensive capability kit".
At an out-of-the-way shack, a surfer mills about with the vial in plain sight. When it falls on the floor, it begins to bubble and leak. Meantime, Five-O scours the area to figure out who may have taken the vial. Kline and Wanda hang out at her apartment, he's nearly given up. Five-O catches a break but it's too late for the surfer, who is suffering the effects of the 'Q Strain'. His surfing buddies can only tell Five-O his name is 'Kit' and lives in an abandoned shack somewhere. Kit is able to get to a phone and calls the operator, getting Shirley. She notifies the authorities immediately and McGarrett moves into high gear.
Shirley also calls Wanda who in turn tells Kline about the vial. They leave to go to the "phone booth on the Kapua Highway". McGarrett and Danno show up first, assessing what's going on. Once Kline and Wanda arrive, the girl on the scene points toward a general are where the shack is. Kline takes off as McGarrett prevents Wanda from following. Meanwhile, Chin and Kono arrive with an HPD unit; McGarrett orders the highway closed in both directions and evacuate as necessary. McGarrett eventually follows where Kline went with an Army decontamination unit.
Kline runs to the shack, he has to determine if it leaked or if Kit opened it. If it was the latter, everything on Oahu will die. The vial is leaking; Kline picks it up and runs with it just as McGarrett and the Army arrive. After Kline buries the vial, he realizes he's been contaminated and he's as good as dead. However, he has time to tell McGarrett to burn the shack.
As the shack burns, Kaye and Dr. Benjamin arrive and are blocked by the Army from getting any closer. The 'Q Strain' must be destroyed; there is no longer a choice. Kline backs from the spot where the vial is as McGarrett and the Army move in to burn the vial. The vial is destroyed but at a high price: Dr. Alexander Kline is no more.
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