How and why Thomas Granger came back was deliberately made vague in the film. As per an interview with Shane Carruth (Primer writer and director, and also the actor who played Aaron) (emphasis mine):
Q: Does everything add up, or did you deliberately leave a few loose ends?
A: It’s never tidily summed up, but I’ve made sure the information is there. Almost every detail, from who the narrator is to how many Aarons there are in the end. But there’s one piece of information that isn’t, and that has to do with [potential funder] Granger coming back and how he was able to. That’s purposely vague. Abe and Aaron each have a point in the film where they find themselves in someone else’s past, and they both react a little differently to it. This is Abe’s moment. This man has found out about the machine and he’s used it to come back, but they don’t know from what point in the future or who told him about it. That’s what spurs Abe to reboot the whole thing, that’s how he reacts—let’s redo everything and then I’m the one in control. It was important that the audience be in the same place that they are—there isn’t any way to know. That’s the one big question that comes up, and I’m satisfied by that—that’s supposed to be the big question. I stuck with the rule that we were going to be with Abe, that we were going to see his experience. Although the narration is coming from Aaron, we only know about Aaron’s experience from voiceover and flashback material, mainly because there was no way to tell a story from multiple points of view dealing with multiple histories.
On Thomas Granger being in a coma after he went back in time, Shane Carruth had this to say (emphasis mine):
Q: Can you elaborate on the concept of recursion in terms of time-travel paradoxes?
A: I have a degree in math and my favorite subject was non-linear dynamics. You have an equation y = x, and you take that answer and feed it right back in for x, and you chart this and sometimes you get fractals and sometimes you get orderly systems. The idea of recursion and whatever it leads to—that informed a lot of the story, the idea of creating a feedback loop. This isn’t really addressed in the film, but the reason Granger is unconscious is because he’s suffering from recursion. What I think happened is that Abe told Granger about the machine. This man who’s been told by Abe about the machine uses the machine to come back and somehow has an interaction with Abe so that now Abe probably won’t tell him about the machine and yet he still finds himself there. Without coming out and saying it, the film is built on the idea that these paradoxes are a way to understand things. The universe is not going to explode or break down if you create a paradox. Whatever’s going to break is probably going to be you.
Source: "A Primer Primer", The Village Voice
The most likely reason why Thomas Granger went back based on information provided in the film is due to an emergency involving Rachel:
Aaron: Can you think of any reason you might?
Aaron: Sometimes we do things but don't know how we got to that point.
Abe: No, I can't.
Aaron: Can't what?
Abe: I can't think of any reason why I would.
Aaron: Well, I can't either.
Abe: What if it was an emergency?
Aaron: So you'd do it if it was an emergency?
Abe: No, I don't know. What, so you might then?
Aaron: I don't know. What kind of emergency?
Aaron (narration): The permutations were endless.
The above was a dialogue between Aaron-2 (hooded Aaron) and Abe-2 on Friday morning (before they went back to Monday morning). We, the audience don't know the exact reason as even Abe-2 and Aaron-2 (the narrator) are not sure what could've happened to cause them to tell Thomas about the time machines. When Aaron-2 and Abe-2 discuss possibilities on why they'd tell Thomas Granger, they hinted that they could tell him about it if it was an emergency, but they are unsure as the "permutations were endless", as Aaron-2 narrates.
Based on their conversation, and on how Aaron-3 (white jumper Aaron) resolved the matter, it is likely that Thomas-2 went back in time because of an emergency involving Rachel and it seems that this might have something to do with Rachel's ex-boyfriend hurting or killing Rachel (in Thomas-2's iteration/loop). He either wanted to resolve the situation himself, or wanted to tell Abe and/or Aaron about it (and get them to resolve the situation).
To resolve the situation, Aaron-3 tried to get Rachel's ex-boyfriend arrested and sent to jail on the night of Robert's birthday party.
Aaron-2 [hooded Aaron, speaking as the narrator]: And that's where I would have entered the story. Or exited, depending on your reference.
Because when Aaron came back the second time, it wasn't so easy.
He wasn't expecting me to put up a fight. And by that time, he was too exhausted to take me.
But for reasons that are only evident to me now, I understood that he simply wanted it more. That he just had more invested. So I left.
He had already performed the task, as I had intended to... of recording the conversations of the day just in case.
Through that earpiece he had a three-second lead on the world.
As per the above dialogue by Aaron-2, he realized that Aaron-3 (white jumper Aaron) is better suited to resolve the situation. "He [Aaron-3] simply wanted it more. That he just had more invested. So I left." So even though Aaron-2 overpowered Aaron-3 when they fought, he left and allowed Aaron-3 to do what was needed.
Based on Aaron-3's actions, resolving the situation has something to do with getting Rachel's ex-boyfriend arrested and sent to jail on the night of Robert's birthday party.
Aaron-2 (speaking as the narrator):
I can tell you with certainty what I did that night when it was my turn.
But I think it would do little good, because what the world remembers, the actuality, the last revision is what counts, apparently.
So how many times did it take Aaron as he cycled through the same conversations lip-synching trivia over and over?
How many times would it take before he got it right? Three? Four? Twenty?
I've decided to believe that only one more would have done it.
I can almost sleep at night if there is only one more.
Slowly and methodically, he reverse-engineered a perfect moment.
He took from his surroundings what was needed and made of it something more.
And once the details had been successfully navigated there would be nothing left to do but wait for the conflict.
Maybe the obligatory last-minute moral debate until the noise of the room escalates into panic and background screams as the gunman walks in.
And eventually he must have got it perfect and it must have been beautiful with all the praise and adoration he had coming.
He had probably saved lives, after all.
Who knows what would have happened if he hadn't been there?
From this dialogue by Aaron-2 where he talks about Aaron-3, we learn that the last "revision" to the reality is what counts. He also surmises (because he already left town when Aaron-3 was at the party) that Aaron-3 could have tried many times to resolve the situation right and that "eventually he [Aaron-3] must have gotten it perfect." This most likely resolves the whole Thomas Granger paradox / comatose situation.