After rescuing Marty in 2035 from Officer Griff Tannen, and preventing him from getting a sage implant and a personality rewrite by Commissioner Wilson, Jennifer drove the second DeLorean time machine back to March 4, 1986.
Doc dropped Marty and Jennifer off at the McFly residence, and left a bag of canisters so that Marty could contact him in his secret lab if he ever needed help. Doc then took the DeLorean back to 1893 to reunite with his family. Unfortunately, Marcus Irving, a scientist who had worked unsuccessfully on time travel for the United States Army since 1963, witnessed the DeLorean breaking the time barrier. He was jealous of Doc Brown, as he felt that he had taken years away from his life by not taking the temporal research position with the Army.
Shortly afterward, the police arrest Douglas J. Needles for crashing into the delivery truck. They don't believe his claims that Marty McFly and Jennifer Parker were involved, since there was no DeLorean near the crime scene, and Marty and Jennifer were both asleep in their beds.
Needles used his phone call to call Marty a chicken, and Marty was unfazed, telling him that he needed to change his tune.
The next day, Marty and Jennifer saw the new Clint Eastwood movie, and Marty arrived home in the late evening. His parents admonish him for being late, but he hugs them, and lets them know that he is finally over his depression caused by Doc's absence.
On April 13, Marty wrote a new song for the The Pinheads to practice playing. Paul, Bobby and Lee stop playing and laugh, as the events that Marty is singing didn't happen. Marty tells them that he remembers it, as it is when they went camping and Bobby first joined the band. His band mates tell him that they didn't take a bus, but instead took Marty's truck to the campsite. They state that was the whole reason for the trip, as Marty was saving up all summer to buy the truck, and his dad pitched in the remaining money.
Marty looks at photos and talks to his girlfriend about how they first met, and realizes that his memories don't match up with a lot of events. He then decides gets theories about time travel from his father, and his father takes him to talk about fate with his priest, Father O'Flaherty. The latter causes Marty to worry about going to hell, as he and Doc are changing God's divine plan.
On April 15, He picks up Jennifer and shows her the Twin Pine Mall, explaining that Doc was originally shot and killed by Libyan terrorists, and that he saw another Marty get in the DeLorean and travel to 1955. He worries that he is not the same Marty that she fell in love with, but Jennifer kisses him and says that she can tell that he is the same person by his eyes.
Marty and Jennifer decide to go to Doc's secret lab, as Doc is the only person who can help with a matter related to time travel. The alarm has on the secret lab sounded and two police officers are there. The older officer, Officer Foley, recognizes Marty from the ordeal with Needles. The officers are aware that Marty knows Doc, and wonders if he can turn off the alarm.
Marty uses the keypad to disarm the alarm, and the four of them enter the lab. One of the officers asks if he should turn off the temporal field generator Mk II, since it is making a funny noise. Marty and Jennifer respond simultaneously with "no", realizing that the machine must stay on in order to ensure that Marty and Doc would return from 2035.
Marty spots a canister marked with a zero. He opens it and finds a note signed "a friend in time". Soon, Marty comes face-to-face with Marcus Irving, and learns that he left the note. Irving revealed that, after his project was terminated by the United States military, he used an inexpensive Yugo GX to create a partially working time machine.
He feeds Marty a story about their being multiple universes with multiple versions of himself, and states that he is from another universe that still exists, which is why his memories don't match. Marty gets worried and writes a letter to Doc and leaves it in a canister.
- Marty took the band members of The Pinheads on a camping trip in his truck instead of a bus, and he met Jennifer Parker differently in this timeline. He worries that he is taking the place of the "real" Marty from this timeline, due to his conflicting memories.