He knew that a little part of Scott blamed him for the whole lycanthropy thing, heck, Stiles blamed himself a little too. However, even with ADHD he was able to focus on helping Scott through it, being there for him throughout everything. He made allowance after allowance when Scott got a girlfriend, made the first-line for lacrosse, wolfed out; Scott had always made massive concessions for him throughout his life because, hey, it isn't easy living with ADHD or not having a mum. Stiles knew what Scott had done for him over the years, and so he may have felt a little lonely when Scott was out playing tonsil hockey with Allison, or he was out tracking with Derek or just generally being a wolf, but he put up with it and tried hard not to begrudge him – after all, it was his fault.
Somehow though, the grudge started to grow. It wasn't just feelings of loneliness when Scott was with Allison - which was all the time, by the way – because hurt was starting to be thrown in the mix and when Scott was ignoring his emails for days at a time, the feeling of rejection crept closer still. Despite this, Stiles still mentally defended his friend against his own accusational thoughts, still kept up the pretence of best friendship with the only friend he'd really had. It wasn't until the kanima was circling around the swimming pool as Stiles held Derek up for nearly two hours that he started to reassess his friendship with Scott.
There had been signs that the friendship was drifting, being pulled further apart by each member within it, but when Stiles called, requiring help because his legs were f*cking tired – holding another guy, one twice your size, up for like 120 minutes can do that – and he really couldn't handle treading water for another 20 minutes let alone 2 hours still supporting Derek's weight, and Scott hung up on him, it was time to finally see the truth. He had plenty of time after he had dove underwater, letting his phone drop to the bottom, saving Derek instead and then continued treading water to really think about what was left of their friendship.
Even after the evaluation, Stiles still helped. He followed and researched and followed further. He almost destroyed his relationship with his father as he chose Scott's security over his own, time and time again. He practised magic with Deaton so he could protect not only Scott but Derek's pack as well. He lied to his father so he could have Scott's back, like he always had. He risked his own neck just so Scott stayed unhurt throughout it all. He disregarded his own safety trying to save the only friendship he'd ever really experienced.
Then Gerard happened and he broke. As Stiles was being kicked by an old man, somebody quadruple his own age, he realised that Scott was unlikely to be the one who came to find him. As he felt pain in his ribs and back and pretty much everywhere, he knew that Scott probably didn't even realise he was missing. As his sanity cracked slightly with every hit, he understood that Scott wasn't about to kick through the door to rescue his butt. That recognition hurt more than the pain Gerard Argent was inflicting; had he and Scott really drifted so far from one another?
Just like that he had a new resolution to himself, an aim to get his life back on track and stop pining for Scott. He was still going to help the wolves, protect the pack and even see this kanima problem through to the end, but he wasn't going to rely on Scott, he couldn't unless he wanted his heart to be thoroughly torn. It felt like drowning, it really did, as he drifted through this feeling more alone than ever, like he was trying to breath in but the pressure was too much. He tried to ignore it the best he could, taking deep breaths in, remembering his father throughout it all.
Then Scott came back to him. He was back to where he began only wolfed out as he lost Allison and lacrosse but found Stiles. Except he didn't find Stiles because though Scott was present in Stiles' life, he wasn't present. When Stiles had envisioned the return of his best friend, it was meant to release the pressure on his chest, ease the pain of his heart. Instead, he found he was the one reassuring the other and he was comforting him, as if he had no problems of his own. He went along with it, telling Scott that he still had him, that he was a constant in his life, and even though it was only a half truth, not only did Scott believe it but he wanted more.
He had Scott back, with Scott being the same as before, yet it was abundantly clear that Stiles wasn't the same. Stiles had for months been waiting for Scott to come back to him, realise he needed him, but when he hadn't, Stiles had changed. He had closed a large part of his heart off, closed a bit of him off, so that the hole Scott had left wouldn't hurt as much, and he couldn't suddenly open it. So he lied to Scott – and if he were honest, to himself – pretended that everything was fine and that they could be best friends just like before.
The pressure didn't release from his chest and breathing didn't come any easier. He still felt lonely and hurt and rejected; he didn't think this was going to change for a while because though Scott was there in person he wasn't there in likeness. He was leaning on Stiles, only he had already leant too much on Stiles without taking any of the weight back. Stiles pushed it to the back of his head, ignoring the thoughts belittling his friend, trying to just appreciate the presence of Scott. Stiles was suddenly back to making allowance after allowance for his friend.
He knew that a little part of Scott blamed him for the whole lycanthropy thing, heck, Stiles blamed himself a little too. Who was Stiles kidding? Stiles blamed himself a lot for it. Maybe if it was all his fault – the lycanthropy, by association the lacrosse/girlfriend and the distance - it would be easier to forgive Scott.