This one is rather sad. Based on observations of Season 2, episode 1-4.
They were drifting apart. Every day, it seemed as though the gulf grew just a little bit wider, the distance just a bit more difficult to navigate. For a while, Kurt told himself that it was just his imagination. Or that maybe they were simply too busy to spend as much time together as usual.
He knew this was a lie.
At the end of Sophomore year, they had been so close it was like having a twin. It did not matter that he was a skinny, white, gay boy and she was a plus-sized, black, straight girl. They shared a special bond. It was more than having the same movie crushes, favorite foods, and the like. Sometimes they could almost read each others' mind. He knew when Mercedes' self-esteem needed a pick me up. She knew when he was lonely or frightened. They knew how to make each other smile and there were no secrets between them.
Then Quinn Fabray had moved in with Mercedes and Finn Hudson had moved in with him. Each new arrangement had lasted for less than a month (less than a week in Kurt's case) but they were each affected by those changes more profoundly than they had expected.
Kurt found himself warier to extend his trust and, for the very first time, reluctant to tell his best friend his troubles. His blow-up with Finn was the bitter end to a school-year's worth of hopes and dreams that predated his friendship with Mercedes. It was something too terrible, and too painful, to share with anyone. So, he remained silent, simply telling her that things had not worked out.
Another reason he could not talk to her was that Mercedes had started moving toward a strengthening of her already-deep faith in God after spending so much time with Quinn. Seeing the other girl's struggle with her life and her own faith, witnessing the miracle of human birth first hand, had made Mercedes introspective and thoughtful. It was something that was clearly too personal to share easily and Kurt could not bring himself to ask. He tended to avoid the subject of religion, not sure how his fellow students would greet the news that he was an atheist.
Summer had come between them next. Mercedes had spent most of those three months visiting relatives in D.C. and Kurt had devoted much of his own time to working at his father's garage. His father's defense against Finn had moved him deeply and he felt the need to strengthen the family bond they were rebuilding, a bond that had not been so strong since Kurt's mother died.
Mercedes and Kurt phoned and texted regularly over the summer, but rarely for more than a few minutes at a time. Conversation dried up more quickly when there was no high-school gossip chain or common experience to connect them.
When Junior year began, their relationship had seemed to be getting back to normal. Kurt's wounds had mended, if not entirely healed, and he was able to laugh and chatter over fashion, music and boys again. Mercedes had mentioned volunteering at her church and he was glad to realize that the secular and spiritual compromise did not interfere with her desire for an active social life.
The first few weeks of school passed uneventfully. They tried and failed to recruit new members for Glee, there was a fight to perform Brittany Spears that had resulted in Kurt throwing what even he had to admit to himself was a PMS level hissy-fit; and eventual victory to perform their chosen song that was later ruined by the sexy number causing an actual riot within the student body.
Kurt chose to ignore his continued distance with Mercedes, pretending that it did not bother him that she chose to sit with Quinn or Artie or some other club member at least as often as she did him. After all, they were her friends too and she had every right to spend time with them.
Then Kurt's father had a severe heart attack. He fell into a coma and for a week and a half, Kurt felt like he was living inside of a nightmare. He could not think, or react, or feel anything separate from the all-consuming fear and anger of knowing that he could lose his dad at any moment.
Then the others had started bombarding him with prayers; offers to pray for Dad, to pray for him, to sing spiritual songs that were obviously about making themselves feel better, but doing absolutely nothing for him. When he had admitted that he was not a believer, he had seen shock, dismay and even disgust filling various pairs of eyes.
Mercedes was the worst of all. She had looked at him like he had just confessed to a love of torturing small animals. Even before his confession, she had claimed that she did not know what to say to him.
Those words had cut Kurt like a sharp blade. "I'm sorry this happened. What can I do? C'mere, baby, let it all out." Were the words she would have uttered without a second thought last year, or could have simply conveyed with one of her warm, one-of-a-kind hugs, now beyond her? Was he so far from her thoughts that they never even occurred to her?
And then she had gone behind his back, after he had specifically stated that he did not want prayers, and joined Quinn and Rachel in their unwanted prayer-vigil at his father's bedside. They had invited Carole and Finn to join them, but never even told him what they were planning. He might have even allowed it if anyone had. He did not believe, but that did not mean he was incapable of appreciating a caring gesture.
The question was, why did nobody care about how he felt? Why did his best friend no longer care? Had his lack of faith done what the revelation of his sexuality had not, and driven her away; made him disgusting to her?
That was the real reason he had given in to Mercedes' request that he attend her church service. He did not want to go. The entire experience had been uncomfortable and embarrassing, and it had not changed his views on a higher being at all, but Mercedes had been so proud and hopeful and sure that he would have an epiphany and start believing. He had smiled and hugged her, thanked her for what she had done, all the while feeling his heart twist with pain that he had been forced to offer comfort while feeling none.
Kurt's dad had emerged from his coma and was on the road to recovery. Taking care of Dad provided a welcome distraction from Kurt's other troubles, but he found himself avoiding Mercedes. Their bond no longer seemed so solid. His trust in her love and understanding felt broken and empty.
Desperate to make their relationship feel normal again, he invited Mercedes to sit with him during Glee. For a while, conversation was flowing nicely. She shot him a friendly insult over his new shirt – saying it looked like Christmas wrap for a bondage-gift – and he was starting to feel better. Then, he had made an effort to initiate a gossip session about the new boy. There was little doubt in his mind that the absurdly blond quarterback was gay, or at least questioning, but his saucy comment to that effect was quickly dismissed.
When Mercedes casually asked who he wanted to sing his duet assignment with, Kurt suddenly realized to his own dismay that he did not want to utter the, "Why, you, of course!" that would once have been a natural response. Not that they ever did sing together, but he should have jumped at the chance, shouldn't he? Instead, he had decided to pursue the quarterback. Stupid history repeating itself, and that idea had quickly turned around and bit him in the ass. By the time he had been left partner-less, Mercedes had teamed up with Santana and the two of them barely spoke to each other again.
They congratulated each other on great performances, exchanged a sorrowful look at not winning the prize, and that was it.
Suddenly, without quite knowing how it had happened, they were friendly but no longer quite friends.
Kurt wondered if they would ever get that relationship back.
How could they even start?