That sure is a lot of plutonium you've got there. What will you do if you don't use it all up by the time Marty's girlfriend changes from Claudia Wells to Elizabeth Shue?
I've watched Back to the Future many times. A few years ago while watching it probably for the hundredth time I did something I hadn't done before: I counted how many times the plutonium was used as fuel. Then I went back and counted the number of vials of plutonium Doc Brown had.
Hey Doc Brown, umm, what did you do with the rest of that plutonium by the end of the movie? A vial of plutonium can only provide enough power for a single trip through time. A round trip through time requires at least two vials. So what happened to the rest of the plutonium?
After Doc Brown's dog Einstein jumped one minute into the future riding in the DeLorean the case of Plutonium is shown on-screen. One vial is already empty in the upper left-hand corner of the case and it can be deduced that the vial was used to fuel the DeLorean's nuclear reactor in the aforementioned experiment with the dog.
After pulling out second vial from the case on-screen and refueling the DeLorean Doc Brown prepared to travel into the future but realized that he had forgotten the case of plutonium in his truck. Libyans showed up killing Doc Brown and Marty escaped back to 1955 without any plutonium for a round trip.
That's two vials of plutonium used so far out of twelve.
Because Marty McFly and past Doc Brown used lightning to get the required momentary power for temporal displacement the count still remains at two vials after Marty returns back to 1985.
After returning to 1985 the DeLorean breaks down forcing Marty to rush back to the mall to try to warn Doc Brown that the Libyans were coming to kill him. Yada, yada, Doc Brown drives Marty back to his house and Doc Brown proceeds to 2015.
By the way, even though this isn't the alternate 1985 with corrupt Biff Tannen the off-screen third plutonium refueling of the DeLorean demonstrates how useless the 1985 Hill Valley police department is. Remember, the DeLorean broke down in the Hill Valley Courthouse Square after returning back to 1985. After revealing his bulletproof vest there would have been an off-screen scene of Doc Brown and Marty loading up the truck, driving away from the mall that had a bunch of dead Libyan terrorists in the parking lot, arriving at Courthouse Square, putting on radiation suits, refueling the DeLorean's nuclear reactor -
... and all of this happened after Marty crashed the DeLorean into the Assembly of Christ Church in downtown Hill Valley.
Back in 1955 a Hill Valley PD patrol officer noticed a "weather experiment" and checked to make sure that Doc Brown had a permit. Apparently a damaged church and two guys in radiation suits working on a DeLorean isn't out of the ordinary for Hill Valley Courthouse Square in the early morning hours of 1985.
Image Source: YouTube
By my count three vials out of the twelve were used by the time Doc Brown showed up with the Mr. Fusion upgrade to the DeLorean in the movie.
So where did the leftover plutonium go? I don't think Doc Brown just chucked the plutonium into his new Mr. Fusion. The "fusion" part implies that matter below the atomic number of iron is converted to energy. As Wikipedia states:
For elements lighter than iron on the periodic table, nuclear fusion releases energy. For iron, and for all of the heavier elements, nuclear fusion consumes energy.
The actual name in canon of the product manufactured by Fusion Industries is the "Mr. Fusion Home Energy Reactor". I don't believe many homes in 2015 Hill Valley would have had plutonium as a part of their household waste and plutonium would most likely voided the warranty if anyone tried.
In the Back to the Future comics a few more vials of plutonium can be accounted for. The fourth vial was to go back to 1938 to buy a copy of Action Comics #1. The fifth vial of plutonium fueled the trip to sell the comic book. The sixth vial of plutonium was used to go back to 2015 for the Mr. Fusion and hover conversion upgrades to the Delorean.
That still leaves half of the leftover plutonium unaccounted for.
My headcanon is this: While in 2015 researching what was considered valuable and had appreciated in value Doc Brown found out about bitcoin. After reading that the last bitcoin was expected to be minted around the year 2140 Doc Brown used his knowledge of making a DeLorean nuclear to invent an autonomous nuclear powered mining rig for bitcoin and established his own mining farm off-grid to run for decades.