It's the night that Troy leaves, when they start fucking. And maybe Annie would never actually say that word, but that's definitely what's happening. There's nothing sweet or romantic about it. It's just anger and fear and resentment and hurt. It's something to feel so they don't feel the pain.
After Troy leaves, Abed goes to the blanket fort, by himself, everyone shuffles off, not sure what to do next, and Annie has nothing to do but to follow Abed. He stares through her, blankly, unable to cry, but he does explain, "I don't like change. I don't want him to be gone. People always leave me." Annie knows this is about losing his best friend but also all those other friends who couldn't help him and also about his mother and her new family. All Annie can do is hold him, and even as she murmurs things about Troy not leaving voluntarily, and him nobly sacrificing himself for the group, and how they should be proud of their friend; she still feels the fear and the anxiety herself.
In this moment, she can't think of any of the good times she's had so far in college, all she can remember is people not wanting her, being too young, too high strung, too much of a goody two shoes. Nobody thinking she's good enough except this group and especially these two boys who invited her to live with them, and thought she was good enough to spend time with. Good enough to join in their games even though she didn't always do it right and her British accent was awful. They were patient and they just kept including her. So she's afraid, too. She's afraid that Troy leaving is just the first sign of the whole group splitting up, that the best friends she's ever known in her life will all just go their separate ways. If she has to lose Troy, she can't stand to lose Abed, too.
So she does the only thing she can think of, which is to lean in and kiss him. For the first time not in character, she feels Abed respond beneath her lips, and he presses back, anxiously and uncertainly, filled with the desire to know that at least one person wants him, doesn't want to leave him. So he's the one who deepens the kiss, and leans them back onto the bottom bunk. Then it's hard to tell who's the one who takes the next step, removes a cardigan or undoes a belt. But they both want it so badly, and they both want it to block out anything else.
It's not sweet and it's not romantic, but at that moment, it's exactly what they need. Afterwards, they're both exhausted, and that's perfect so neither of them has to think. They curl up together in the blanket fort and try to find some peace.
The next morning, neither of them really make a big deal of it. They wake up and decide who gets the bathroom first, and what kind of cereal should be for breakfast. If it's more awkward than it's been since the first week Annie moved in, it's only because Troy isn't there. They never talk about it, either what happened, or if it would happen again, and in fact, no one ever says 'Oh hey, I'm feeling low, let's have sex', but it happens again and again, almost every single day for the next few weeks. Annie climbs into the recliner with Abed, straddling his lap and pressing pause on the remote so they don't miss a second of Inspector Spacetime. Abed unable to sleep in the middle of the night because it's too quiet, so he gets into Annie's bed instead. So much silence while they make dinner that they start kissing, and the kissing turns into Abed lifting her onto the counter, then turning the oven off with one hand and removing her panties with the other.
What they lack in comforting words, they make up for in moans of pleasure. Abed feels more comfortable than he has with any other woman he's been with, because for the first time, he knows exactly what she's feeling, and feels the same. It's for comfort, so he takes what he wants, and gives it in return. It's fiercer than Annie's used to in her limited experience, but she turns her anger into passion and meets his hips with her own and leaves scratch marks on his back.
Every thrust is a chance to forget and every kiss is a promise, "I won't leave you."
It works well enough for about a month. That's when it evolves, and it's not really just about sex or comfort anymore. They distract themselves with other things and one day they're done the puzzle Troy asked them to finish. Annie presses the last piece in and Abed wants nothing more at that moment than to capture her mouth with his. He's not the best at impulse control or filtering his thoughts, so he does it, and she enthusiastically returns the action, assuming it is because they can't contact Troy, can't tell him it was a tugboat, but truthfully as Abed slides his hands under her dress, he is only thinking of her and her smooth skin and the sounds she makes as she comes.
The thought that he might actually be able to move on is just as disturbing as the loss of Troy, and Abed's mood spirals downward. He won't leave the apartment and he won't go in the Dreamatorium. His friends visit and he gives one word answers and stares blankly. The only person he's at all honest with is Annie, and he still can't talk to her about what is really on his mind, can't ask 'would this have happened anyway' or 'do you regret this' or 'is there any way you might possibly love me?" He sees that she's happy to spend time with him, and that she gets interested, passionate even, about the shows he likes, and he notices when the kisses and caresses get more tender and maybe even loving, but he shoves it all to the back of his head because if he got to be with Annie, really actually be with her, he would be happy. And that would make him a traitor. He can't be happy without Troy. The bond he had with Troy is so integral to his being, not even the best girlfriend in the world could make up for its loss.
She's the only thing keeping him sane because he can't imagine not having her to reach for in the night, but she's also driving him crazy because there's got to be a timeline just like this one except Troy didn't have to leave, and in that timeline Annie never kissed him. He doesn't see any timelines where he gets both Troy staying and Annie's kisses. He can't be happy, so he thinks he must be broken. A few days before the summer semester ends, he tells her he can't do this anymore, and retreats into the blanket fort, alone. In that moment of weakness, he texts Britta to say she can try out her therapy on him. He knows he won't be able to cling to sanity much longer.
For Annie, it had stopped being "just sex" for a while, at some point she started watching him eat, mesmerized by his long fingers gripping the spoon. At some point, there was nothing driving her to kiss her way down his stomach other than the desire to watch his face when she took him in her mouth. He thinks he's her second choice, or maybe even third, but truthfully, Annie thinks he is worth a million Jeffs and wants desperately to see him smile again.
She sometimes thinks she could survive the group breaking up if she could just keep him with her, and she pushes this traitorous thought to the back of her head, because at the end of the day friendship is definitely more important than sex or romance, especially when you can't tell if you are imagining the romance part and the object of your affections is very fragile and hates change. She'd continue as they are forever rather than ask him for more than he can give and lose him. She leaves the apartment without Abed, and the group still gets together, but it isn't the same and no one is happy. There's no one she is willing to burden with another worry, so she turns back to her biology textbook and tries not to think about the world crashing down around her or how much she personally misses her good friend Troy, who she could talk to about anything and who always made her laugh.
When Abed tells her it's over, she feels like the wind is knocked out of her, and he walks away during that moment of silence. She's too timid and hurt to follow and demand answers, so instead she goes into her room and cries as softly as she can so Abed won't hear through the thin wall.
She worries so much because he won't talk to her anymore but she hears him leave his room in the night, open the door to the Dreamatorium, and talk to himself. It's almost a relief when Pierce and Shirley explode at each other and she has something else to think about. She's worried more than ever when he enters the courtroom wearing a felt goatee and wielding something she knows is a bonesaw because the ninth Inspector used one against the Skeleton king in the only episode she really disliked. Whatever he had planned is put on pause because Jeff is making the Winger speech to end all Winger speeches, all about friendship and love and goodness and helping others. Abed's eyes flicker between Jeff and Annie as he absorbs the words. The group would make it. There's still happiness and love to be had in the world. Annie's eyes fill with proud tears but her heart really fills when Abed, without goatee or bonesaw, sits next to her. She doesn't care what it means as long as it means he is still there and won't be blank anymore, she clasps his knee and he covers her hand with his.
When Troy shows up, it's almost too much joy to handle, and the biology final seems easy compared to the two months of pain that came before. The seven of them stay up entirely too late drinking and planning the two week break before fall semester, and although Annie and Abed really need to talk, they are happy just to have everyone they love in the same room. Troy moves back in the next day, and when Britta goes to help get bags out of the car, Abed stops pulling tape off the Dreamatorium walls long enough to lower his head to Annie's and kiss her. He keeps his hormones in check because all of their friends are in the other room, but also to show it isn't just sex. He pulls back and tries his hardest to show all of his emotion through his facial expression. Annie runs her hand up his arm to stroke his face, love shining in her eyes, too. By dinnertime, they still haven't had a chance to talk, but it isn't really necessary since Annie grabs the seat next to Abed so they can hold hands under the table. When the pizza comes, Abed volunteers to go downstairs and get it, and as he springs up, he kisses her quickly on the cheek, right in front of everyone. After all of the catcalls from Pierce and "awww"s from Shirley and Britta, and Jeff high fiving Abed on the way out, nothing even needs to be said between them until the night, when Abed slips into Annie's bed. "I love you", she whispers. He touches her hair, gently tangles his fingers in it. "I'll never leave you", he promises.