Tony and Doug tumble to the ground in a South Pacific jungle. Tony sprains his ankle upon impact and as they check his injury, they hear the sound of men working in the distance. The two scientists find World War II Japanese soldiers moving out of a compound, while American naval vessels open fire on the island. Doug and Tony take cover and Tony tells Doug to go off on his own because his injury will only slow them both down.
Doug refuses to abandon his friend and the two men find a shack in the jungle. Doug peers in through the window and spots a room with a radio. However, an elderly Japanese soldier opens fire on him. The soldier's rifle jams and Doug easily subdues the man. Sgt. Itsugi speaks English and tells Doug that he's the only one there. He offers to take care of Tony's injury and Doug brings his friend in. While Itsugi wraps the sprain, Doug goes into the shack's other room, a store room, and confirms that it's empty. Itsugi explains that he's a spotter and that the rest of the Japanese troops have just evacuated the island.
Tony suggests that he use the radio to contact the American fleet and call for a pickup. However, a younger Japanese man, Lt. Nakamura, sneaks in behind Doug. Using a stick to pretend he has a gun, Nakamura convinces Doug to surrender and then takes his gun. Laughing, Nakamura derisively dismisses the two Americans as "Joes" and says that he will soon kill them.
At Project Tic-Toc, Swain and Anne lock on to their friends' coordinates and watch as Nakamura threatens Doug and Tony. Unable to pinpoint the scientists' exact location, Kirk has his team focus on the nearby American fleet. He identifies the Missouri and the Illinois and tells Anne to check the records and determine which operations contained both ships.
Nakamura sends Itsugi out to get some equipment and then sneers at the older sergeant's traditional decoration. Doug informs the lieutenant that they're non-combatants but Nakamura says that he doesn't care and that they might have had better luck claiming to be missionaries. Tony tells him to shoot them if he's going to shoot, but Nakamura shoots Itsugi's decorative flower and then orders Tony to stand up so he can tell if the young man can walk. Tony hesitantly gets to his feet and Nakamura orders them out of the shack. When Itsugi returns, Nakamura tells him to shoot the Americans if they try to flee and then goes out into the jungle.
As they wait for Nakamura to return, Tony tells Doug to run while he jumps Nakamura. However, his friend refuses to abandon him. Nakamura returns with two bamboo staffs, having put a nail in the end of his, and explains that he went to Stanford in the U.S. He learned kendo there and tells Tony that they will fight a duel. If they refuse, he'll kill them and if they win, they only have to deal with Itsugi. Tony asks what the rules are and Nakamura attacks him and says that there are no rules. Despite his injury, Tony fights as best he can but Nakamura soon defeats him. When he asks why he shouldn't kill Tony immediately, Doug points out that if he wanted them dead then he would already have shot them. Nakamura concedes that Doug is smarter than he looks and asks if Doug will beg for his life. When the scientist refuses, Nakamura is satisfied since that would ruin his game, and informs them that he has more in mind for them.
Doug asks if Nakamura plans to give them a chance to live and the lieutenant explains that Tony's injury means that the scientists have an even chance against Nakamura and the elderly Itsugi. He wants to stage his own private war and the scientists will participate because they need to get to the radio. The American forces will soon secure Iwo Jima, unaware that the Japanese are preparing a surprise aerial bombardment. If Doug and Tony don't warn the American fleet then thousands of American soldiers will die. Nakamura gives Tony and Doug a one-hour head start to flee into the jungle and improvise whatever weapons they can. If they win, they can use the radio. Doug wonders why Nakamura is prolonging their deaths and the lieutenant claims that he's paying them back for what the Americans did to him.
The scientists have no choice but to play Nakamura's game and head off into the jungle. However, Doug suggests that they change the rules and double back to the shack before their hour is up. Tony is against the idea, pointing out that they can't change history, but Doug insists. The younger scientist realizes that Nakamura has gotten to Doug, but Doug says that they don't have a choice and Tony insists on going with him.
At the project base, Kirk realizes the same thing as Tony has. Anne uses Nakamura's description of the attack on Iwo Jima to pinpoint their friends' location to one of two nearby islands. They need to identify the landmarks they can see through the Tunnel and Swain calls the Pentagon to have them find a Japanese officer who survived and bring him to Project Tic-Toc. While they make the call, Kirk gambles and tells his team to concentrate their efforts on the southernmost island.
Doug and Tony go back to the shack and Doug circles around to the back to enter the storeroom. He pries the door open and slips inside, and manages to grab a rifle and five grenades. Itsugi comes in and Doug hides behind some crates. Nakamura comes in and grabs a bottle of wine, and then mocks Itsugi's obedience to his superior officer. He asks why Itsugi doesn't kill him and the sergeant says that it's not his place to do so. As they talk, Doug notices a tarantula crawling up his chest but is unable to move and brush it off. Once Nakamura and Itsugi finally leave, the scientist brushes the spider off. However, as he leaves he disturbs some crates. Nakamura runs after him but Doug makes it back to Tony.
Realizing that Doug has stolen some grenades, the lieutenant stands in the clearing outside the shack and dares the unseen scientists to kill him. However, he points out that they might destroy the shack and the radio, dooming the American fleet. Despite that, Nakamura steps further away from the shack. Doug prepares to throw the grenade but Tony points out that Nakamura could still spot them as they throw and get off a shot. Doug reluctantly helps his friend back into the jungle, while Nakamura fires some random shots into the jungle and then goes back inside.
At Project Tic-Toc, Anne and Swain realize that Nakamura has a death wish. The Pentagon calls to inform Kirk that their friends are on the southernmost island, just as he guessed. They're also sending a survivor, a doctor who survived the war and was on the island, to help them pinpoint landmarks so that they can lock onto their friends and bring them back.
In the jungle, Tony suggests that they use a grenade to rig a booby trap. Doug agrees and the two of them use a vine to rig a tripwire.
The officer arrives at the base but tells them that because of a personal matter, he is unable to help them. However, when Kirk explains that two lives are at stake, the surprised doctor agrees, admitting that the saving of lives trumps his personal issues. They show him the image of Itsugi in the Tunnel and the doctor knows the sergeant. However, he tells the team that Itsugi was the only man left behind on the island. When they show him Nakamura, the doctor stares in shock and then tells them that the lieutenant is his son... who died when the American overran the island. Overcome, Dr. Nakamura faints and a medic is called in while Anne maintains a lock on their friends.
The scientists carefully tie the primed grenade to a tree and they set off a grenade, forcing Nakamura to investigate. The lieutenant and Itsugi come down the path but Nakamura spots the vine, throws the grenade away, and then fires into the jungle. Doug throws a grenade back at him to cover their escape and Nakamura figures that they only have two grenades left. Itsugi is reluctant to kill outside of a battle and a disgusted Nakamura sends him back to guard the shack.
At Project Tic-Toc, Dr. Nakamura tells the team that his son was a kamikaze pilot. Because of his time in the states, the young lieutenant was unable to bring himself to finish his suicide mission. He crash-landed and was brought back to the island, where he was given the chance to commit seppuku and atone for his dishonor. However, Lt. Nakamura refused and he was left behind when the island was evacuated.
Doug and Tony get to the harbor and wonder if Nakamura told them the truth about the Japanese attack, or just said it to provoke them. They spot scout planes overhead and realize that he was telling the truth. Tony, the only one who can operate the radio, finally takes one grenade and tells Doug to stay at the harbor until he comes back. As Tony limps off, Nakamura arrives and spots Doug. The lieutenant opens fire, forcing Doug to retreat into a nearby cave. Doug throws the fourth grenade at Nakamura, wounding him in the leg. As Nakamura binds his wound, Doug suggests that they declare a truce and go home. The Japanese soldier hysterically yells that he has no home because of his dishonor and that they must kill each other. Desperate, he limps toward the cave, hoping that Doug will kill him. When Doug is unable to, Nakamura begs the scientist to kill him.
At Project Tic-Toc, Dr. Nakamura demands that the project team bring his son back. They warn him that they can only safely bring back two people but Nakamura refuses to help them with the landmarks unless his son is one of them. Kirk realizes that Dr. Nakamura isn't bluffing and reluctantly agrees to bring back whichever scientist is closest to Nakamura when they initiate the time-transfer. The general warns Dr. Nakamura that his son's psychological problems are insurmountable, particularly after a 23-year time-transfer, but the Japanese officer remains resolute.
Lt. Nakamura assumes that Doug is dead and limps off to the shack. Meanwhile, Tony sneaks into the shack and discovers that Itsugi is gone. He goes to the radio but the sergeant fires at him from the storeroom and destroys the radio. The sergeant charges into the room and Tony manages to knock him out. However, he discovers that the radio is beyond repair.
At the base, the team watches as the American landing force arrives at the island. Dr. Nakamura reminds Kirk of his bargain and the general has Anne and Swain focus on the radio shack.
Lt. Nakamura returns to the shack with Doug in pursuit. Tony comes out with Itsugi's rifle and Nakamura fires at him, forcing the young scientist into the jungle. Tony throws his grenade at Nakamura and it lands at the lieutenant's feet. He stares at it, half horrified and half accepting, and then kicks it away. It turns out to be a dud and he laughs hysterically and goes into the shack. Meanwhile, Doug finds Tony and they update each other on what happened. Doug takes the rifle and calls to Nakamura, assuring him that he'll make sure he is treated honorably in American hands. Itsugi wakes up and, hearing Doug, asks the lieutenant whether he will choose an honorable death or a shameful life.
Anne locks onto Tony and Doug but warns Kirk that they are equally close to Nakamura. She wants to risk the triple-transfer but Swain insists that any attempt will kill them all. Kirk has no choice but to choose which scientist he will save. However, in the Tunnel screen, Lt. Nakamura removes a ceremonial sword from his chest. Realizing what his son plans to do, Dr. Nakamura tells the others that his son has finally chosen the path of honor. He releases Kirk from his vow, telling him to bring Doug and Tony back while Lt. Nakamura kills himself.
As American troops storm the beach, tony and Dog watch as Nakamura staggers out of the shack, wearing ceremonial robes and carrying the sword. He calls out, telling the scientists that it's kill or be killed, and prepares to shoot into the jungle at them. Doug prepares to shoot back but finally realizes that he can't do it. Before Nakamura can fire, a shot rings out. One of the invading Marines saw the enemy in the white robes and fired. Tony and Doug run forward and identify themselves as Americans, and then go to the dying Nakamura. The lieutenant says that he's finally remembered that he's Japanese and dies. The Marine wonders what Nakamura was doing, wearing white robes and making himself a target, and Doug tells him that the lieutenant was fighting a private war... and won.
The Tic-Toc team initiates the time-transfer and Doug and Tony tumble through time and land in an alien control chamber. Two silver-skinned aliens teleport in and direct the scientists to a translation circuit. Once they can communicate, the alien leader tells says that they are aliens from Alpha One. They are conducting a test raid against Planet 16 and show a picture of their target: Earth. When Doug tries to stop the aliens, they shoot him down and tell Tony that they will leave Earth a dead world.