Doug and tony land at the Japanese Consulate in Honolulu on December 6, 1941. The consul, Tasaka, is supervising his men Sumida and Okuno in the burning of the code papers. The scientists claim that they're sightseers who wandered into the consulate but Tasaka doesn't believe it. He orders them out but then tells Sumida to follow them since they must be spy. Tasaka doesn't want to risk killing them on consulate grounds and tells Sumida to dispose of them if they do anything suspicious.
At Project Tic-Toc, the team watches the entire exchange and realizes that Doug and Tony have arrived in Pearl Harbor one day before the surprise attack by the Japanese. They try to get a time lock without success.
As they leave, Tony and Doug figure that the staff was burning secret codes in anticipation of the attack. Tony tells his friend that he was seven years old and living in Honolulu with the attack occurred. After his mother died, his father, Commander Anthony Newman Sr., moved to Hawaii. Commander Newman disappeared during the attack and his body was never recovered. Tony suggests that they should find Commander Newman and find out what happened to him, and possibly warn him about the attack. Doug wonders where they should go and Tony remembers that he spent the day with his best friend, Billy Neal, and his father came over for dinner that night.
When the two scientists arrive at the Neal home, they tell the servant girl, Yuko, that they have important business there. As they wait to see Billy's mother Louise, Tony tells Doug that his father is the same age that he is now, and that the house was destroyed in the attack. Louise comes in and tells them that Commander Newman stopped to pick up Admiral Brandt and is running late. She assumes that Tony and Doug are there to tell her what happened to her husband, who is serving aboard the Enterprise and will arrive at Pearl Harbor the next morning at 8.
Sumida, who has followed the scientists there, goes to the back door. Yuko, a spy for the Japanese, lets him in and they watch from the dining room as Tony, Doug, and Louise talk. The butler, Ichiro, approaches the dining room and Yuko warns Sumida that the butler is an American sympathizer. Sumida kills him and hides the body.
Commander Newman arrives and tells Louise that Brand is running late. When he sees Tony, he finds the young man familiar and Tony admits that they met a long time ago. He tries to warn his father that his life is in danger without giving specifics, but Commander Newman insists and Tony finally tells him that the Japanese are planning a sneak attack. While they talk, Sumida and Yuko listen in and realize that Tony and Doug know their exact plans.
Tony's father informs him that the Japanese fleet is nowhere near Hawaii. However, Tony explains that the Japanese High Command has sent a third of the fleet to Indochina to draw the Americans' attention while the rest of the fleet head toward Honolulu. Commander Newman wonders how Tony knows what he knows and Tony informs him that they are there because of time travel. His father dismisses him as a lunatic but is interrupted when Billy and Young Tony run in and ask to stay up late. Louise reminds them that they promised to go to be don time, while Doug and Tony realize that the children will be there when the house is destroyed. Tony starts to tell Commander Newman who he really is, but Yuko comes in and tells them that Ichiro went home because his wife is sick. The commander tells Tony and Doug to go to the states if they're worried about an attack and tells Yuko to usher them out.
As Yuko takes Tony and Doug out through the dining room, Sumida captures them at gunpoint and take them out. Meanwhile, Kirk and the others watch the abduction but then lose their lock and catch a glimpse of the Japanese fleet heading for Honolulu.
Tasaka and Okuno meet Sumida at a Japanese import company and tie up the two scientists. The consul doesn't believe their story and has Okuno administer truth serum to Doug.
Admiral Brand arrives at the Neal home and Commander Newman tells him about Tony's story. Brand says that the Japanese fleet is heading for Indochina and Commander Newman points out that Ton y told him the same thing. The admiral figures that it was a lucky guess and that Tony is just one of the dozens of doomsday predictors in Honolulu. Despite Brandt's assurance, Commander Newman tells Louise that he's going back to the base to check on something.
Doug continues to tell the truth under the influence of the sodium pentathol and describes the Japanese plans after Pearl Harbor. Tasaka is happy to hear that Japan will be initially triumphant, but his happiness turns to distrust when Doug tells him that they will lose at Hiroshima. Before Doug can explain further, Tasaka tells Okuno to give Tony truth serum. Tony tells the consul that he'll save the thing and angrily asks if he should tell them about the atomic bomb.
At the base, Commander Newman goes to the naval communications center. Lt. Tom Anderson confirms the report about the Japanese fleet near Indochina but the commander tells him to confirm with Washington.
Tony tells Tasaka the same story under the drug and explains that they gained access to his office through the Time Tunnel. Tasaka assumes that the scientists are U.S. spies but figures that they're brainwashed to believe their claims about time travel. Sumida reports that Commander Newman didn't believe their claims about a Japanese sneak attack and Tasaka tells Okuno to find and kill the commander. He leaves for the consulate to contact his superiors for orders and tells Sumida to guard the scientists.
Ichiro's wife calls Louise to ask where her husband is, and Louise is surprised to hear that Ichiro didn't go home like Yuko claimed. She checks the dining room and finds drops of blood on the carpet. Okuno storms in and demands to know where he can find Commander Newman. He searches the house and prepares to go into Billy's room, but Louise grabs a gun. Okuno runs off and Louise calls Commander Newman at the base. He tells her that he'll send a marine guard to protect her and the boys, and a relieved Louise breaks into tears.
At Project Tic-Tac, Kirk and the others continue watching the Japanese fleet and the approaching planes. Swain tries to get a lock on Tony but focuses on Young Tony for a few moments before concentrating on Tony and Doug. The fix drifts and Kirk speculates that if Young Tony dies in the attack then their Tony will disappear from existence.
Tony and Doug check the wall clock and realize the only have an hour and fifteen minutes until the bombing begins. Tasaka calls and Sumida steps into the office to answer it. Once they're alone, the scientists turn back-to-back and untie each other. When Sumida and two of his men return with orders to kill them, the scientists fake being tied up until they get close, and then jump them. Doug takes out the other two men while Tony ties up Sumida long enough for both scientists to get away.
After Commander Newman leaves for a few minutes, Louise calls the base and asks for him. Anderson tells her that the commander has stepped out and she asks him to tell Newman that she sent the marine guards home because everything is all right. Once she hangs up, Commander Newman comes back and Anderson gives him Louise's message and tells him that Washington has confirmed that the Japanese fleet is near Indochina.
At the base, Jerry tells the others that they have to do something to change history. The scientists tell him that there's nothing that they can do to stop the attack because it's already happened and is a part of history.
Tony and Doug get to the Neal home and tell Louise that her home will be destroyed in thirty minutes. She assumes that Commander Newman sent them and they tell her to take the boys up into the mountains. When Louise hesitates, Doug accurately predicts that Yuko didn't come to work because she's a spy and knows about the coming attack. Convinced, Louise agrees to take the children to safety. Billy comes out and tells them that Young Tony just ran out when he overheard what they said. Tony tries to remember what happened that morning to his younger self but realizes that the shock of the attack blocked out his memories.
Doug figures that Young Tony went to the base to warn his father. Tony runs after his younger self and catches him, and tells him that he wants Commander Newman to live as much as Young Tony does. He promises to warn the commander and tells Young Tony to head up into the mountains with Louise and Billy. Doug runs up and Tony asks his friend to take Young Tony back and make sure that they all get to the mountains.
Doug and Young Tony return and leave with the Neals. The Japanese begin their attack and Doug makes sure that they're all clear before going back for Tony.
At the base, Anderson takes two military policemen to the consulate to arrest Tasaka as a spy. He runs into Tony, who gets directions to the base. However, after Anderson leaves, an explosion collapses a wall on Tony, knocking him unconscious. Meanwhile, Anderson and his men arrest Tasaka and his men just as Doug arrives. Doug takes the consulate car and drives to the base to find tony.
At Project Tic-Toc, the team watches as Tony wakes up and Doug arrives. The two scientists drive for the base.
As Commander Newman tries to warn the Enterprise away, a bomb hits the communication center, bringing the ceiling down. The radio is badly damaged but the bomb doesn't go off. It's still ticking and Kirk in the others realize that it could go off any second. Jerry tries to relocate the bomb to another time zone. Swain and Anne stop him, warning that they have no idea how many innocent people they could kill. However, the transfer goes wrong and the bomb appears in the Time Tunnel. Swain confirms that the Time Tunnel will send it back automatically in 90 seconds and Jerry and Kirk go into the Tunnel to defuse the bomb. While Anne and Swain try to hold it in their own time, the two men do what they can and move off. The bomb disappears but Jerry warns them that he doesn't know if they disarmed it.
Doug and Ton y reach the command center and find Tony's father, dying on the floor. Doug repairs the radio and the commander pulls himself up and sends the signal to the Enterprise to turn back. As they confirm the order, Commander Newman turns to Tony and asks who he is, and Tony admits that he's his son. The commander is satisfied that his son will survive the bombing and dies happy. Crying, Tony holds his father for a moment and then leaves with Doug. The bomb detonates behind them, destroying the building and destroying Commander Newman's body... and assuring the future Tony knows where his father is never known. Another bomb lands nearby and the desperate Tunnel team initiate a time transfer, pulling Tony and Doug out just in time.
Tony lands alone in a swamp and two redcoats run past without seeing him. They open fire and Tony runs off. He finds a campsite with two sets of buckskins, steals them, and hears Doug land nearby. The two of them link up and don the stolen clothing. Doug concludes that they're somewhere in the southern United States in the middle of a war zone. The redcoats double back and spot them, and Tony and Doug run toward the American lines. Doug trips and one of the redcoats draws a bead on him...