One of the biggest questions of the film that is never fully explained. We will first break down the sequence of events and then explain the motives behind each from a human and Thing perspective. Sequence of events: (1) Blair runs the computer program and discovers the possible threat the Thing poses, (2) Blair kills all the sled dogs and destroys the tractor (off-camera), (3) Blair destroys the helicopter, (4) Blair injures Windows and destroys the radio, (5) Blair is locked up outside in the shed, (6) Mac is questioning Blair in the shed as to the whereabouts of Fuchs, and (7) Blair has clearly been assimilated: he is building a ship, attacks Garry, etc.
Now, the question is asked, why would a human Blair kill the dogs and destroy everything? At this point, it is very clear that Blair understands the situation and feels that his comrades do not. He is afraid that the Thing will escape and infect the entire planet. He kills the dogs, destroys the helicopter, and destroys the tractor to isolate the men. Although Blair says, "no dog can make it a thousand miles to the coast," he was more or less referring to a dog on its own, and not a team with a master. He may have also killed the dogs to prevent infection when we see Clark at the dog kennel sorrowfully looking at a dead dog with a fire axe in it's neck, though we know that an axe would not be sufficient enough to prevent that - keep in mind that Blair has lost his sanity at this point. Blair destroys the radio so that no outside help can be reached; it could be another way out. If this was the case (that Blair was assimilated after his lock-up), it was either Palmer or Norris that got to him while he was locked up in the tool shed. Somewhere during the 48-hour period that Mac refers to on his tape recording would seem logical.
The Thing perspective: The Blair-thing would have destroyed the tractor, radio, and helicopter to prevent the men from escaping and to keep them from reaching outside help. The dogs were killed to make his motives seem more human. The Blair-thing's plan worked; he was seeking isolation so that he could build a craft to escape. This makes it look as though the Thing's intentions are not to assimilate the entire Earth, but to simply get off the planet; had the Thing wanted to assimilate the entire planet, it could have just as easily stolen the helicopter as Palmer and fly to the nearest base, country, whatever but this assumes that the thing would only be able to pilot a helicopter as Palmer but this does not seem likely as it is building some kind of craft as Blair/thing.
Just before being locked up, Blair tells Mac to watch out for Clark. Again there are two plausible possibilities as to what he meant, depending on whether he was infected yet. If Blair was still human, then it would have likely been that since he knew how the Thing worked, he deduced that since Clark had been isolated with the Dog-Thing for a long period of time, there was a very strong chance Clark was infected. If Blair was a Thing, then he would have been trying to throw Mac off, drawing suspicion towards a man who was still human whilst the Thing continues to infect the team.
Another possible, but remote, theory is that Blair was infected during the autopsy of the Burned Corpse-Thing or the remains of the Dog-Thing. It was a cellular infection which took some time to gain control of his body and "conscious" mind. The Thing gained more control as the cellular infection increased over days. We know this is a considered by Blair. As the infected individual's body is slowly taken over, they remain conscious during this state but unaware that they are infected, but their actions are subtly influenced by the Thing's ever-increasing hold over them. Blair destroyed the dogs, tractor and chopper. The dogs being killed was a completely human response backed by his scientific knowledge that any one of the dogs could have been inadvertently infected during their attack in the kennel cage by hostile or cellular infection. In his destruction of the tractor and chopper, the Thing influenced his decisions.
Think about it... The Thing was a masterful strategist. It had been alive for eons and assimilated hundreds, maybe even thousands of beings and intellects, a theory referred to by Fuchs when he has his private conversation with Mac about Blair's notes. Many of its actions had a two-fold and even three-fold win-win situation that still gave it an edge in the final game. Yes... Blair destroyed the tractor and chopper to prevent the infection from spreading to populated areas (human response), but he also destroyed them to hide the fact that he had stolen parts from both. The crew was less likely to investigate a smashed, ripped-apart tractor or chopper to see that all of the parts were there. Blair was well aware of military protocol and knew that his mental breakdown would call for them to isolate him, giving him time to assemble the parts and build a craft to get him to the nearest populated area. The craft was never meant for long distance travel. A third goal in destroying the tractor, chopper and communications was to prevent anyone from getting out until they were ALL infected. Military protocol would have been to capture and quarantine all parties involved until it was determined who was human and who was not. The Thing could not take the chance of someone contacting the rescue team and revealing the alien infection. However, Blair was not the only one who may have been infected by cellular means during the autopsy... Fuchs may have also been infected!
We see Blair performing the autopsy and Fuchs "sniffing" and going through the clothes of the Burned Corpse-Thing and other items there. Those garments and items are soiled with possible dried blood and other body fluids. Fuchs is seen standing there listening to Blair while going through the items without gloves or other personal protective equipment. Since the scene ends this way we can assume that Fuchs assisted Blair in other ways during this autopsy even if it was just "Hold this" or "Move that." Cellular infection is HIGHLY probable at this point. This theory would also explain Fuchs' disappearance. By the time he talked to Mac, he knew that cellular infection was a strong possibility. Blair at this point was isolated and locked up (or so we thought), but Blair was secretly moving about the camp collecting and assembling the last of the parts and tools he needed to finish his craft. It is very possible that it was Blair who killed the power and walked past Fuchs' door in the dark. By the time Fuchs got outside to chase this suspicious person, he found Mac's undergarments.
If cellular infection was possible, by this time Fuchs' actions would be influenced subconsciously as well, since he was infected during the same time period as Blair. Thus, after finding Mac's undergarments, Fuchs heads to Mac's shack, possibly planning to snoop around for more proof that Mac was infected before accusing him publicly (clearly a human response). While there, he stuffed Mac's shorts in the oil furnace, this being a subconscious influence by the thing to keep an ally hidden. In all likelihood, Fuchs began to question his own actions on the walk back to the main compound and came to the realization that he "must" be infected to have just done such a strange thing rather than exposing Mac. The Thing only attacks when discovered or "attacked." Why wouldn't a self-realization spark an attack as well? At this point during Fuchs self-realization, the thing begins to reveal itself, going for a more quickened "hostile takeover" of Fuchs rather than the cellular option. As Fuchs begins to change and lose the last of his humanity, he does the only thing he can, setting himself on fire in the snow.
Another hint that Blair has been infected before he destroys the radio and communications equipment is that his intentions, as 'the thing', are to destroy any means of communication (radios) that will allow the remaining humans of the research outpost to contact the outside world and warn them of 'the thing' that they unleashed from the ice. Blair, as 'the thing', could prevent the humans from warning the rest of the world to either proceed with caution when approaching the arctic facility, or to isolate or even destroy the facility from afar. Once Blair, as 'the thing' was completely sure that the existence of the creature was safe and only known to the remaining humans in the facility, 'the thing' could take as much time as it needed to slowly and surely assimilate the rest of the crew.
While Blair may have been infected on a cellular level when he autopsied the first remains of the thing early on in the film, it was slowly infiltrating his entire body, copying him slowly, to the point that Blair might have realized what was going on, causing his intense paranoia, enough to where he breaks down completely and attempts to kill everyone and destroy the communication equipment.
The theory of cellular assimilation is possibly debunked by what happens to Bennings. The dog runs up to him and licks him, in theory this would be enough to begin cellular transformation yet he is the first on screen aggressive assimilation we see. If he was already being infected on a cellular level which is easier to hide why would this be necessary?
A sign that Blair was himself when he was first quarantined in the outdoor shed by the others was that when MacReady and the others talk to him from outside the shed door to ask the whereabouts of Fuchs, we see that Blair had hung a noose from the ceiling, possibly in an attempt to hang himself before the thing had time to take over. Perhaps he realized that his remains would still have cellular activity and he figured suicide was pointless. Perhaps he just couldn't bring himself to do it. Or perhaps he made the noose intending suicide, then his mind was finally assimilated and the thing stopped him from taking his own life. It's also worth noting that in the same scene, Blair tries to talk Mac into letting him back into the main camp. The Blair-Thing was clearly taking advantage of its isolation, so it seems strange that it would run the risk of joining back up with the rest of the men, since he would not be able to continue working on his craft without drawing suspicion. Thus it would be logical to say that Blair was human (or at least in the process of being assimilated) at this point; he really did feel bad about his actions and want to leave the shack.
But the other alternative is that the noose was a ruse. If Blair was a thing at that point, he would want to give the appearance of being normal, while still remaining isolated. A human Blair would, naturally, want to come back inside. But he would have to come up with a way to prevent that, without looking suspicious so he could keep working on the underground spaceship. If you were human, and trying to plead your case that you're recovered, would you leave something as obvious as a noose hanging over your shoulder? It has the same effect as saying you're sane while eating a bug.
It's entirely plausible that Blair rigged the noose as an insurance policy on the off-chance that the men would decide on their own to let him back in, or talk to him at some point. He begs to be let back in, but anyone talking to him would be able to see the noose hanging behind him, and would then assume that he's still not all there. MacReady certainly notices it, as after Blair's normal conversation and outward appearance of being back to normal, his only reply to Blair about being allowed back into the outpost is a rather non-committal, "We'll see", followed by cutting him off mid-sentence as he further pleads to be let back inside.
One theory that Blair has been infected early on is that he deliberately gets himself isolated by acting insane and out of control. Once he's alone in the cabin, outside of the surveillance of the other remaining crew members, he can begin digging the tunnel under the shed and building his ship that will allow him to escape to the mainland, or possibly even to outer space.
In the original story, "Who Goes There?" on which this movie is based, the character or Blair has a nervous breakdown and they isolate him in solitary confinement in a cabin. Like the movie, the short story never states when exactly Blair was assimilated, but it is possible that he was assimilated beforehand and fakes the nervous breakdown. In the cabin, the Thing, in Blair's body, begins building an anti-gravity device to get back into space, or to leave Antarctica, but before it can complete it, the other crew members realize what is happening and they kill the Blair-Thing before it could complete its objective.
Carpenter and Producer Stuart Cohen have indicated that their plan was for Blair to have been infected at a very early time, as he is in Campbell's short story. Cohen goes on to indicate that MacReady's line upon the discovery of the spaceship, "Blair's been busy out here all by himself" is to indicate that Blair was a thing for quite awhile, long enough to have adequate time to build the spacecraft.
It's also worth noting that between the scene where he runs the computer simulation, and the time we see him again destroying the radio room, the yellow button-down shirt he was wearing has disappeared. The theory is that the thing rips through your clothes when it takes you over, so the disappearance of the shirt between the two appearances could definitely be because the shirt was destroyed in the take-over. We certainly see that the take-over destroys clothing, as Windows sees Bennings' destroyed shirt and vest in the storeroom after seeing Bennings in mid transformation.
Fuchs tells MacReady in the Thiokol Snowcat that Blair "Locked himself in his room and won't answer the door." The assumption is that he's despondent after running the simulation, or is prepping for what he's about to do, but it's also possible that after running the simulation and taking the gun, he was surprised by Norris or Palmer and assimilated during that time. As we see when Blair attacks Garry, all Norris or Palmer would have to do is be standing outside Blair's door and put their hand over Blair's mouth to prevent a scream, and the assimilation would already be happening. Then they would just lead Blair back inside and lock the door behind them. That would explain why Blair loses the shirt he's been wearing all along prior to the radio room rampage.