First time Reid meets Morgan he is a bit intimidated by a man's puns and his cocky smile. He knows this type, and no matter what Gideon says, he prefers to be cautious. Just in case. He's used to being made fun of and to not being taken seriously. But Morgan makes it go away in a terrifyingly short time. He looks at Reid with a mild admiration instead of a usual annoyance, when he spontaneously bursts into statistics, or makes geographic profile on a scratch of paper, or quotes files and books he read long time ago. It's nothing special, Reid has been doing it as long as he can remember (and he can remember a lot), but that's like the third time in his life when someone actually full heartily admires his abilities without feeling intimidated and thus in a need to fight back. Morgan is nothing close to what Reid initially thought he would be.
Morgan is easy going, kind and good humored, he's great with kids, great with animals, great with women… he is just generally great. He makes Reid feel relaxed and safe and at home. But he changes when there is a dangerous situation. When someone - anyone - is in a prime danger, Morgan becomes snappy and even aggressive. He insists on being assigned to the most dangerous part of investigation, he is the first in knocking doors and putting himself on the line of fire, he even ignores orders sometimes. It's like Morgan doesn't quite trust them to protect themselves so he prefers to keep it under control by taking the heat himself. And oh how angry he is when someone gets hurt anyway.
Reid is best friends with JJ, and Gideon is like a father to him while Hotch is like an older brother both of whom he has never really had. And Garcia… well, Garcia is a fellow nerd, sweet and utterly brilliant. But with Morgan it's something different, special even. They get each other on a level that is almost disturbing. They shouldn't have this level of understanding, different people that they are. And Reid knows that he gets what he gets because of what his childhood was like. But nothing he knows about Morgan indicates he has had similar experience. And yet somehow Reid knows that Morgan is also damaged. Also hurt. Also lost in some way. Reid knows that despite his solid appearance Morgan is fragile. His overprotectiveness, his anger, his frustration when situation goes out of control - Reid is familiar with them far too good. He wonders who was it exactly that Morgan lost. You don't ask such questions, Reid knows as much, so he keeps quiet.
On the train case Morgan almost loses it when Reid proposes to go and trick unsub himself. He has neither power nor moral authority to say this, it's not his call, but nevertheless Morgan explodes with "I forbid you" and "You are not going there, Reid" without a shadow of hesitation. If it was anyone else, Reid would take this as questioning his abilities to do his job. He wouldn't stand it. But that's Morgan, and Reid can see just how much does he care and how much he can't stand putting anyone in danger, so he answers calm and gently. He reassures Morgan with all he has that it's the only way, and that he will be fine. He doesn't even object when Morgan puts a vest on him while repeating things Reid already knows very well. If it helps Morgan to deal with stress, it's ok, - thinks Reid. And then he goes to the train and kind of betrays Morgan by not keeping his promises. It's not like Reid has a choice if he wants to save hostages, but still…
Afterwords Morgan doesn't even talk to him until the next day. He doesn't even come close. He is so angry and tense Reid can feel it from a distance. And he also feels that Morgan tries very hard not to snap on him, not to be completely out of line with a colleague who did successfully close the case after all. Reid gives him his space and time to calm down. That's just another proof of how badly Morgan deals with even a potential loss.
Reid doesn't initially think it's about him. Morgan is overprotective with almost everyone: from victims to all mighty Hotch. But the more they know each other, the more he realizes it is about him after all. Morgan is just different with him in his reactions: more intense, more honest, more easy to burst. Maybe it's because Reid's the youngest. Maybe it's because he looks fragile and awkward. Maybe Morgan also feels that deep inside they are similar.
Reid trusts him - intuitively at first and then, after the nightmares talk, he trusts him consciously. He trusts him because Morgan really cares about him and even if sometimes it means trouble - that's just Morgan. He needs to know he's done everything. Reid gets it. He also trusts him because he wants to gain Morgan's trust and it's a two ways road. It should take time but he hopes that someday they'll be close enough for him to be able to help with the damage.
He certainly doesn't expect the rape story, though it completely makes sense. Now he knows who is it that Morgan lost. Morgan lost himself, he lost a feel of control over his life and he also lost faith. Reid tries to hate Carl Bufford for what he did, but he fails, he isn't very good in hating. He is just so damn sorry that it happened. Especially that it happened to Morgan. Morgan who really is so great and thoughtful and caring but who doesn't let anyone come close enough to really get to know him. Reid saw Morgan in Chicago when they hunted unsub without knowing yet that it's Bufford. He saw him right after. Morgan certainly isn't over what happened. He is still ashamed. He probably didn't even visit a psychologist. He probably never told anyone. All these years he was angry and ashamed and afraid, and he was in it all alone while maintaining his happy-go-lucky macho facade. Reid knows how it feels, he knows a lot about wearing masks and being lonely, and he wants to help. He just doesn't know how, and Morgan doesn't help by closing up immediately after their return to Quantiko.
Soon after that Tobias Hankel happens and there are tortures and drugs, mostly the drugs - long after Hankel is dead... when Spencer finally gets out of it, he isn't even sure he didn't screw it all up. His job, his friends, his life… and whatever this is they have with Morgan. For as much as he knows, Morgan should have been furious and pretty crushed when he found out about the kidnapping. And JJ told him at some point, long after the case, that Morgan actually was terrifying. But now he is totally fine with Jennifer but doesn't even talk to Spencer outside of work. Maybe he is just that much angry. Maybe he thinks that Reid's disgusting with his drugs problem. Spencer would agree on that... but he realizes soon enough that's not the case. Morgan wouldn't judge him, he is better than that. So most likely it's that Reid got too far in being hurt and Morgan simply can't deal with it anymore.
It certainly doesn't help realizing that actually he was the one in fault of JJ being hunted by the dogs, and himself being kidnapped, and also of not going to the rehab right after he got free. He made everyone worry and, knowing how hard it is for Morgan to be in a situation like this when he can't do anything, Reid isn't much surprised that Morgan is distancing himself away. That's only fair. After all Spencer really does attract troubles on his head a lot, and he also isn't very good in dealing with them.
He still can't stay away. It takes a leap of faith to share his fears with Morgan the first time after the kidnapping, but after that he just can't stop. Each time Morgan is so ready to help, and more importantly he gets it all so well it's intoxicating. Maybe it's because Reid is also damaged and ashamed of himself, and now that Morgan surely knows it, he can't deny him of help. Maybe he feels responsible. Maybe it's just how generally great Morgan is, still being there for him when he is requested even though he detached himself from Reid in an everyday life. That's not healthy for either of them, Reid knows it. It would be better to let Morgan step away. He can't. So he pretends everything's fine and tries not to impose himself on Morgan when he can help it. He misses him badly though.
As time goes on Morgan softens on him. Sometimes it's just like it was before the kidnapping. They have their moments: they talk, they joke, they cover each other's backs and argue about stupid things like who is cooler, Flash or Batman. Sometimes Reid catches Morgan staring at him with a soft smile and a strange dreamy look on his face. That never lasts though. Morgan rushes away the moment he realizes Reid noticed. Still, they do more or less fine and though Reid can't come closer he also doesn't feel being pushed further away.
After Gideon leaves the agency, Reid is almost lost. He has been there before with his own father, but he has never thought that Gideon would do that. He didn't even realize himself how much the man meant to him until it was too late. Luckily Gideon knew that long before Reid did. He still left. Reid goes over the note and their talks again and again trying to make sense of it, but all he can think about is that his happy little family illusion is over. Gideon is far gone, Hotch is dealing with his marriage issues, and Elle is lost to the team and doesn't even want to talk to any of them anymore. They still care about each other, maybe even more than before, and they have Emily now, and they still can count as a family. But the "happy" part is gone. Reid comes closer with JJ, and Garcia kind of gets him under her wing, and he suddenly finds a really good friend in Emily… but it's not the same. It won't ever be. Not with Gideon left. Not with Hotch forgetting how to laugh. Not with Morgan so far away. Still, they go on catching bad guys and surviving shootings, reapers and nightmares. They even get closer with Morgan, keeping their bizarre connection alive and sharing moments of the past and thoughts of the present. Most part of the sharing is on Reid's side though. He always thought of himself as of a pretty closed person. Beside Morgan he is a shameless extrovert. But hey, it's still the best kind-of-friendship-but-not-quite relationship he has ever had.
The anthrax case gets them hard. The moment Reid realizes that room is contaminated, he knows he's gonna die. He is fast enough to close the door though, so Morgan is most probably out of danger, which is great, but then it hits him. It's not even that he doesn't want to die - of course he doesn't, and of cause he's angry and scared, but those first few seconds when he sees Morgan's shocked face all he can think about is: "Oh, God, not again". He almost feels how panic grows in Morgan's mind, and he certainly knows how badly Morgan would take being completely helpless and watching him die, and maybe even thinking that somehow it's his fault. He thinks: "I'm so sorry, Derek, I didn't want you to go through this, please be ok and not blame yourself for not coming here first. Sorry for not letting you step out after the last time. Sorry for not being able to let go. Sorry for putting you through this again".
He only says: "Sorry", - but he thinks that somehow Morgan got the sense of it because he doesn't ask any questions, he just stands there tense and rough.
Reid keeps himself busy with the case while he can and after that he just tries to hold on in his denial of drugs despite the pain and troubled breathing. At some point he almost wishes to die already but he can't just leave them behind. Them - meaning his mother who's got literally no one else, and Derek, who shouldn't be on this list apart from the team, but who is still there nevertheless. When Reid wakes up on his way to recovery, Morgan is sitting near his bed, and that's so aright that Reid is only surprised by his own not being surprised few hours later. They don't even talk about it. Reid isn't going to ruin the moment by scaring Morgan away with questions, and Morgan doesn't seem to want to go away. That doesn't last very long.