An explanation contributed

Primer plot summary

Aaron, Abe, Philip and Robert work by day at some major firm and sell home-made electronic products in their spare time. But while they've had some interesting patents, they haven't made major money from the side projects. (In fact it's implied that a man named Joseph Platts stole one of their patents and/or some of their money.) It's been agreed that each guy can put something forward to work on when their turn comes. Robert's idea is to build a strange piece of hardware which can theoretically reduce the mass of an object inside it. This is just after Christmas time (hence Aaron's new refrigerator).
The box requires superconductivity. They can't generate the low temperatures they need, so in the brainstorm session they throw out an idea or two for doing it at room temperature. They cannibalize a catalytic converter for palladium, and build the thing in Aaron's garage.
Later, Aaron and Abe realize that much of the design is extraneous because the device they've built appears to work perfectly. While fiddling with the device, Aaron pokes his hand right the way into the field and Abe puts his hands over it to drop punched holes into the field. This becomes significant later. The box has to be hermetically sealed to outside observation. They flood the box with argon and register the decrease in mass of a blue weeble put inside. Then the box seemingly malfunctions in some way.

*

We then jump forward a little. Now Aaron has done something to the box to make it work properly. In fact, it appears to be putting out more power than is even being put in. After the power is shut off it continues to run for a few minutes. This could be due to the superconductivity in the machine but Aaron and Abe seem to think that it is something else. Aaron and Abe instantly recognize the potentially gigantic applications of the device they have built and decide to cut Robert and Philip out of the loop entirely, saying that the garage has to be fumigated.
Several months pass. They get funding from a Thomas Granger, while Abe establishes a relationship with his daughter, Rachel. (Aaron is of course happily married to his wife Kara, with a daughter, Lauren.) Abe tries and fails to figure out how, exactly, the device does what it does.
Then, in quick succession, quite a lot of things happen. After repeated experiments on the weeble, Abe realizes that a weird fungus is growing on it. He takes it for analysis and is told that the fungus is perfectly ordinary, but the amount of growth he has seen is consistent with years of time passing, not days. He then tries it with his watch and concludes that what they have built is a time machine.
Abe figures out how to build a coffin-sized time machine. He builds what we shall call Box A and places it in a unit at a self-storage facility.
This is now March.

Monday

At 08:30 Monday, Abe primes Box A to activate itself in fifteen minutes. He drives away from the self-storage facility and isolates himself at a hotel in Russelfield. The box activates at 08:45 and is completely powered up at 08:49.
At 15:15, he returns to Box A and switches it off. It takes another four minutes to power down completely. As it powers down, he climbs inside. He waits for what is repeatedly stated in the movie as being six hours - actually it is six and a half. At the correct time, he climbs out of the box just after it was activated (i.e. just after his other self walked away), at 08:45. While his double is sequestered, he goes to Aaron, who is listening to March Madness on an earphone (and continues to do so for the rest of the day). This is the first bench scene.
Abe walks Aaron through the precise series of evidence that led him to the conclusion that the box is a time machine - the fungus and the watch experiment. Finally, at about 15:15 Monday, he brings Aaron to the self-storage facility and they watch just as Abe's double arrives, gets into the box and disappears entirely.
Aaron is now also convinced.

Tuesday

Abe shows Aaron that he cunningly made a single excellent stock trade during the Monday too.
Abe goes through the same routine but this time Aaron insists on following along. By now, Aaron already has his own box built.
They switch on the boxes at 08:30 Tuesday, hide at the hotel all day and then return to the boxes at 15:15. Abe departs the box at 08:45 Tuesday as expected, but Aaron gets jumpy towards the end of the ride, and exits a minute or two early (or, from Abe's perspective, a minute or two late), suffering a severe physical reaction. The time is 08:50 Tuesday morning.
The dialogue during these scenes reveals a few more noteworthy facts.

• Abe and Aaron are both operating under the assumption that there is most likely a single paradox-free timeline. They isolate themselves at the hotel solely in order to prevent the possibility of paradox. In particular, anything that could prevent their doubles from departing the timeline as scheduled would be a major problem since it would result in multiple Aarons/Abes running around, permanently.
• The other important line is "the boxes are one-time use only". What Aaron means by this is that after you have climbed out of a box, you CANNOT go back to it later, switch it off and climb in a second time - because that's what your past self did. You CANNOT use the same box to continuously loop through the same day.
  After a great deal of thought, I have come to the conclusion that this is not actually true. For the purposes of this plot summary, however, all we need to know is that Aaron and Abe both believe this is true and operate under this assumption.
  

They make some more money on the stock market and that evening they have a slightly drunken conversation with Aaron's wife Kara about the prospect of having unlimited money. Aaron raises the hypothetical of punching Joseph Platts in the face, then going back in time and making it so it never happens. Abe says they "can't do that", not because it's morally wrong to punch Joseph Platts in the face, or because Aaron can't tell Kara about the time machine, but because at the moment they are both operating under the assumption that history cannot be changed.
"But the idea had been spoken. And the words wouldn't go back once they had been uttered aloud."
Kara also mentions a mysterious noise in their attic. Birds? Rats?

Wednesday

The same routine again.
They argue at the supermarket and the gas station that morning about paradoxes, free will, paranoia and predestination - specifically, the problems of living in a predestined universe which was made that way by somebody else. At the hotel, and then later on Wednesday afternoon at the library, Abe and Aaron discuss the problem that Aaron is keeping the time machines secret from Kara. They also discuss the problem of keeping them secret from Robert and Philip, and agree to give them a certain amount of patent rights and/or equipment and/or cash in order to salve their consciences instead.
They loop back in time as normal. At 08:15 Wednesday, shortly after getting out the machine, Aaron is bleeding from his ear.
That day, make their successful trades. In the afternoon, they finally admit that the garage has been "sprayed", and work at the garage with Robert and Philip resumes. Robert and Philip have now received their gifts from Aaron and Abe.
Robert reports an interesting story. It seems that Monday night was Robert's birthday party. Abe wasn't there, but his girlfriend Rachel was there. So was Rachel's ex-boyfriend, who walked into the party brandishing a shotgun. So was Aaron, who by all accounts risked his life to defuse the situation safely.
On Wednesday evening, while Aaron and Abe are outside looking for Aaron's missing cat, Abe is angry that Aaron, a family man, risked his life in such a way, and genuinely confused that Aaron acted so uncharacteristically irresponsibly. Aaron makes excuses and claims that since the discovery of the time machines he is seeing the world differently, referencing their conversations of earlier in the day. But this does not fully explain his actions.

Thursday

The same routine again.
During the day spent at the hotel, Aaron's cell phone rings. It is Kara, asking about dinner. This is a mistake, since Aaron is supposed to be sequestered. Abe tells Aaron not to bring the cell phone back in time with him - this is a perfectly sensible way to avert the possibility of a paradox.
They loop back in time as usual. On the second time through Thursday, Aaron watches a sports match (whose outcome they already know) while Abe eats a muffin. Then, on the way to a restaurant, Aaron's cell phone (which he has foolishly brought back in time with him) rings again.
This is a problem, and a critical turning point in the movie. There are two Aarons at this point (one at the hotel), and, due to Aaron's clumsiness, two of his cell phones (one at the hotel). If the phone in Aaron's hand is ringing then, so Aaron and Abe reason, the phone in the hotel cannot be ringing. Symmetry is broken and history has changed. History can be changed.

Friday

At about 02:00 on Friday morning some kids set off car alarms outside Abe's home. Abe goes to Aaron's house and gets him out of bed. Abe reveals that he has been routinely turning the boxes on at 17:00 and turning them off the following morning.
Abe then puts forward a confusing and potentially dangerous plan to visit Joseph Platts at his home, punch him in the face, then, around 03:00 Friday, to use these boxes to go back in time to 17:00 Thursday and make sure that neither the car alarms nor the punching happen. In theory, as a result, both Aaron and Abe's doubles would stay in bed all night, get into their boxes at 15:15 Friday as normal, and leave this timeline permanently, leaving just one of each of Aaron and Abe behind.
It is not clear whether this plan would work or not.
As they climb into the car, however, they realize they are being followed by Thomas Granger, Abe's girlfriend's dad and the project's main source of funding. Granger has several days' growth of beard on his face - but Aaron last saw him at 18:00 Thursday, when he was clean-shaven. Abe phones Thomas Granger's number and the guy who answers is indeed Thomas Granger... but he's not the guy who is following them. Something really weird is going on. This man is a different Thomas Granger who has come back in time using one of the boxes, probably exiting the box at 17:00 Thursday when Abe switched them on. Aaron runs after Granger and when they get close to one another, Aaron trips and falls while Granger falls completely unconscious. They put Granger to bed at Abe's house; Aaron cannot approach him with actually somehow knocking him unconscious. They check that the boxes are indeed turned on. Aaron proposes shutting them off to see if Granger is inside, an act whose consequences would be exceedingly difficult to guess at. They do not do this.
Why has Granger come back in time? Obviously at some point in the future, Aaron or Abe told Granger about the boxes. Then, something happened to prompt Granger to head backwards in time to this point (the earliest he can go) and start observing them. They conclude that the situation would have to have been a real emergency but they have no clue what it could possibly be. "The permutations were endless." History has definitely changed now that Granger has come back, but they have no way of guessing whether the emergency in question has been fully averted by his brief interactions with them and the rest of the universe - he has only been out of the box for about eight and a half hours.
And so Abe loses his nerve.
It is now revealed that there is a failsafe box, built by Abe, in a second storage unit. This box has been running for 3 days 22 hours - in other words, since early on Monday morning. Abe started the box at about 05:00 Monday, then went back to bed until 08:30 when he returned to start Box A. At roughly 03:00 Friday, Abe returns to the failsafe box, with four days' oxygen and water and a small tank of medical-grade nitrous oxide, enters it and travels all the way back to 05:00 Monday.

Monday again

Abe (now Abe Two) exits the failsafe box at 05:00 and gasses his double in bed with the nitrous oxide. He stashes his double in his bathroom.
Now we come to the second bench scene. As in the first bench scene, Aaron is listening to what is supposedly basketball on his earpiece. Abe Two is ill, after four days of very little food, and in shock, after violently gassing his double. Aaron, however, repeats most of the same lines as last time.
In fact, when Abe faints, it is revealed that Aaron is not listening to basketball. He is listening to a recording of that very conversation. How can this be? The recording must have been made in some previous timeline. This is not the original Aaron. This is not the original timeline. It never was. This Aaron has come back in time from the future.
"At this point there would have been some... discussion."
Aaron and Abe confront one another and explain everything that has happened. This is the most difficult sequence in the movie to follow, partly because of the complexity of the plot but mainly because, due to the lack of CGI, it was impossible to put more than one Aaron on the screen at the same time. The two major discussion points are:

1. How?

   Aaron's line, "They are not one-time-use only. They are recyclable," means that although you cannot re-enter a box you climbed out of, you can bring another box with you, activate it once you climb out, and later use it instead, traveling back to the same moment in time again - or a few minutes later, at any rate.
   In some previous timeline, Aaron discovered Abe's failsafe box, anchored 05:00 Monday. He then got inside the failsafe and used it to go back in time, taking with him a second, folded-up time machine. This is the Aaron with the hood.
   On arriving home at 05:00 Monday, Hooded Aaron set up his second time machine as Failsafe Box B, let's say at 05:15 Monday. Hooded Aaron then went to his home and drugged his double's breakfast cereal milk, then stashed his comatose double in the attic. This is the noise that Kara mentioned on Wednesday night. This means that there are now two Aarons in this timeline, permanently. Hooded Aaron assumed his double's identity and recorded all of the week's conversations.
   Then, he used Failsafe Box B (remember: he cannot re-use Failsafe Box A since he already climbed out of it once) to go back in time to 05:15 Monday yet again. He took yet another time machine with him, which he set up as Failsafe Box C (05:30 Monday). He becomes Aaron Three, with the white jumper, no hood. Aaron Three arrives at his house just as Hooded Aaron has finished drugging and stashing Aaron Prime. Aaron Three tries to subdue Hooded Aaron in turn, but this time he is too exhausted, and Hooded Aaron wins. After a conversation, however, Aaron Three persuades Hooded Aaron to leave. There are now three permanent versions of Aaron: Aaron Prime, who is drugged in the attic; Hooded Aaron, who has left town; and the Aaron we have been looking at since the beginning of the first bench scene, with the headphone in his ear feeding him lines, is Aaron Three and always has been.
   Aaron Three has had a LOT of exposure to the boxes. This is why he began bleeding from his ear on Wednesday, and it also why his contact with Thomas Granger nearly killed him.
   It is Hooded Aaron who is the narrator of the story, or rather the person making the phone call.
   So which box did Abe use to come back in time? Logically, Abe must have used Failsafe Box C, since Failsafe Box A contained Hooded Aaron and Failsafe Box B contained Aaron Three. How did that happen? Aaron must have SWAPPED Failsafe Box A and Failsafe Box C. The box that Abe believed was Failsafe Box A (anchored 05:00 Monday) was actually Failsafe Box C (anchored 05:30 Monday). This is not seen or even alluded to in the film, but it is necessary to resolve this plot hole.
   

2. Why?

   Problems of logistics aside, the last remaining question is why Aaron chose to come back in time so far, sacrificing so much, permanently duplicating himself twice. What is he trying to set right, exactly?
   The key to all of this is the party. It is obvious, though left largely unsaid, that when Rachel's ex-boyfriend walked into the room with a shotgun, things could have gone considerably worse. Aaron Three, we remember, risked his life to successfully defuse the situation. We now understand why he would take this risk. There are two other Aarons in this timeline, one of them being Aaron Prime. Aaron Three does not matter - he is a non-person, a walking dead man, and he has no right to Aaron Prime's family. He has no life to risk.
   If I may jump ahead in the movie slightly, the basketball scene (which takes place sometime in the middle of Monday) is also important. This scene additionally establishes that it was Aaron who originally invited Will, Rachel's ex-boyfriend's cousin, to the party - and that it was Aaron who suggested that Will should bring Rachel's ex-boyfriend with him. In other words, whatever originally happened at the party was indirectly Aaron's fault. He holds himself responsible. This is why he has done what he's done.
   

Aaron Three thought the problem permanently settled. But the fact that Thomas Granger came back in time to 17:00 Thursday indicates that it was not, and something bad was still looming in Aaron and Abe's future. However, it is Monday morning again, and both Aaron Three and Abe Two are prescient now. They decide to engineer the situation to end better this time, with Rachel's ex-boyfriend actually arrested and jailed.
By Monday afternoon, Aaron and Abe are both suffering from the effects of a great deal of time travel - they are unable to write correctly.
At this point, the narrator, Hooded Aaron, reminds us that HE, of course, does NOT come from a timeline where everything worked out perfectly. Hooded Aaron has only been to the party once, and he has only seen how it originally played out. He has no idea how long it will take for Aaron Three to "reverse-engineer a perfect moment". From what we see in the movie, though, for Abe Two and Aaron Three, it appears to work first time. The jealous ex is arrested and jailed. The End.
On Monday night Aaron Three crashes at Abe's house. Abe Two cannot sleep. And with that problem resolved, everybody lives happily ever after.
With the following exceptions.

Tuesday again

Aaron Prime wakes up in his own attic after being drugged for 24 hours by his double. Abe Prime wakes up in his bathroom after being gassed for 24 hours by his double. There are three running failsafe boxes which evidently nobody has thought to shut down, in addition to Abe Prime's original Box A, which hasn't been activated yet but is nevertheless operational. "They'll be building their own boxes in another day. And [Abe Prime] already knows what they built."
Aaron Three and Abe Two wind up at the airport. Aaron is going to steal his double's passport and leave the country, because he can never go home. He has lost Kara and Lauren to Aaron Prime. Abe, meanwhile, is going to stay behind so he can sabotage their doubles' attempts to build the time machines. And, more sinisterly, stay close to Kara and Lauren. And protect them from Aaron Three. What?
And finally, on the other side of the world, Hooded Aaron makes his phone call to Abe Prime. Hooded Aaron explains the entire story, including why they drugged Aaron and Abe, and thus "[repays] any debt I may have owed you".
"You will not be contacted by me again. And if you look, you will not find me." Hooded Aaron hangs up, and begins construction on a time machine the size of a warehouse. The End.

Credited to Sam