The main events of this story take place after the Season 7 finale. (Some spoilers for season 7, mostly canon divergence through season 8) Emily doesn't leave the BAU.
The first time Aaron Hotchner fell in love, it happened so quickly; in a whirlwind of emotions and desire. The moment he saw Haley Brooks, he knew they were meant for each other.
When she died, he was certain that he would never love again.
The next time he fell in love, it was more slowly. It happened so gradually, he didn't even realize it had happened at all. His love for Emily Prentiss developed over the course of several years. He had always been attracted to her - who wouldn't be? Her dark, silky hair, long legs, and almost too-perfect face...and her eyes. Her gorgeous brown eyes.
When she'd first joined the team, he was wary of her. He didn't like change, and her presence made him nervous. He was almost certain that Strauss had something to do with it, which made him trust Emily even less. However when his fears were confirmed, he was pleasantly surprised that Prentiss hadn't betrayed him to Strauss.
That was the beginning: Respect.
She continued to prove herself again and again. She was a brilliant agent. She thought on her feet, making split-second decisions that saved the team more than once. She knew when to be serious and when to let loose. Her laugh was one of the few things that could make him smile.
She was an incredible agent, and an equally amazing friend. The other team members confided in her almost too easily, but she never broke their confidence. She became an emotional sounding board for everyone. Well, everyone except him.
He had grown accustomed to keeping his feelings to himself. It wasn't a bad thing; as Unit Chief over the BAU, he needed some degree of distance in order to be effective in his position. Besides, if anyone were to find out about his self-harm, it could cost him his career.
When Emily was nearly killed by Ian Doyle, the next few months without her was hell. He had to watch his team - his family - grieving, and he wished he could tell them the truth. But he had to keep her safe.
The new guilt, added to the responsibility for Haley's death (which he thought he had buried), made for several relapses.
When she returned, he realized that he could never lose her again.
This was when he started to realize he might be in love with her.
The moment he couldn't deny it any longer was at JJ's wedding. Dancing with Emily, lights shining all around...he allowed himself to feel something for her. He held her body close to his, breathed in the scent of her hair, and felt his heart beat faster. He looked into her sparkling eyes, and thought he saw his feelings mirrored.
The song ended, and he reluctantly let her go. God, how he wanted to kiss her...to touch his own mouth to those perfect lips...but he didn't. He couldn't. She was his agent; it would be unprofessional to say the least. He tried to convince himself that it was the joyous atmosphere that was fueling these feelings; that he had simply imagined the look in her eyes.
But he couldn't get her out of his head.
Alright guys, I'm done setting up the background. The next chapter will contain actual dialogue! Sorry I'm such a sucky writer, hopefully you didn't die of boredom through this chapter.