Reid and Emily had already been in a relationship before she 'died'. This story will only make sense if you've seen 7x01 It Takes a Village.
It's mostly Reid's point of view on his relationship with Prentiss in episode 7x01.
Uses (and sometimes manipulates) canon moments from the episode to create an underlying R/P relationship.
xXx
The emotion he had was happiness. The happiness soon moved over into work mode, as soon as they were told to sit down. Quickly, he realized this was not about Doyle from the furrowed eyebrows on Hotch's face. Then the eidetic memories get fuzzy.
"Seven months ago I made a decision that affected this team," Hotch began. "As you all know, Emily lost a lot of blood after her fight with Doyle. The doctors were able to stabilize her, and she was airlifted from Boston to Bethesda under covert exultation."
The faces of Garcia and Morgan changed immediately. Reid took longer to register what emotions to show. Rossi somehow didn't seem surprised.
"Her identity was strictly need-to-know," Hotch continued. "She stayed there until she was well enough to travel. She was reassigned to Paris where she was given several identities, none of which we had access to, for her security."
Hotch stopped talking and let the room react. Even the walls seemed to change, giving a different tone. It had been dark in there for months, and something wasn't the same.
"She's alive?" Garcia was already tearing up at the mere possibility.
Reid's mind wasn't making sense. He was taking in all the details, but they weren't forming the right picture. "But we buried her."
"As I said, I take full responsibility for the decision." Hotch had not been looking forward to the day he was going to tell them this. Now that it was here, he realized how much it hurt his agents. "If anyone has any issues, they should be directed toward me."
Reid was running on two levels of thought. One was busy trying to process that Emily, his best friend, his lover, was still here. The other was taking in the surroundings. Morgan was the most outwardly upset by the news. He was angry, sad, hurt, and Reid wasn't sure if Morgan was even capable of being happy that she was still alive.
Reid looked at Garcia. She sat with her mouth open, staring at the door. He turned to see a sad, apologetic face standing in the doorway.
"Oh my god," Garcia said. Her eyes were crying, her face was surprised, but she was overwhelmingly happy that her friend was there.
All Emily could do was nod. She wasn't able to talk.
Reid stood. He didn't care that anyone else was in the room. He took this as his moment to see Emily and didn't want to lose it.
"I missed you so much," he squeaked out.
She walked over and hugged him, smiling. She let go long before he wanted her to. "I am so sorry, I really am," she said.
"I—not a day went by that I didn't want to—" she was stopped when she saw Morgan's face. He was probably the one hurt the most over her leaving. He beat himself up for months about not being able to save her.
"Really." Prentiss walked over to Morgan. "You didn't deserve that, and… I'm so sorry." She hugged him, but at first he didn't hug back. And when he finally did, he held no emotion to it.
Reid took that moment to rearrange the thoughts he was having. He realized that he needed to be on track, and he couldn't let this moment get in the way of the case. He had to tell himself that he was just working another case, and it was going to be solved just like they used to.
"There is so much I want to tell you guys," she said. "And I will. I promise. But right now I really need to know what's going on with Declan."
"Emily, was there a man living at the house?" Reid asked.
"Yes, my friend Tom Kholer. He was raising Declan as his own."
"Where is he?" JJ asked.
"I never saw him go in or out of that house," Garcia said.
"He was on assignment overseas."
"But he's alright?" JJ wanted to be sure.
"Yes, he's on his way back now. He got a call from Declan, he called me, and when I landed Hotch told me that you had Doyle in custody."
Reid didn't participate much in the rest of the conversation. He wanted to know when he would get a moment with Emily again. He wasn't sure what he would say, but he wanted to be alone with her.
xXx
Standing in the observation room with Emily was hard. It was painfully silent, and there was so much to say without having an ability to say it.
"Do you know how I felt?" Reid asked. It wasn't an angry question; he said it with sincerity.
"I can't imagine," she said.
"I don't even know how I felt." Reid put his face down. "You know what it was like in that waiting room? To know if you were going to come out or not?"
"I was under, Reid," Emily said, letting out a nervous laugh. She was trying to make the conversation a little happier.
"I was pacing. Drinking coffee. No one was talking." Reid looked at Emily. "After JJ told us, then everyone talked. Not a lot, but at least some. All I could say was, 'I didn't get a chance to say goodbye.' JJ wouldn't let me see you. I know why, now, but then it was…"
"Hard. I know. I don't even know how to say anything to you. Or anyone else." It was Emily's turn to face the ground. "Morgan took it so hard! He spent so long wishing—"
"I spent the same time he did wanting you!" Reid was angry she wouldn't talk to him. He felt like she didn't even care how he felt. "You don't even know how hard it was for me. I wanted to die. And you know what? Everyone important in my life left. My father left. Elle left. Gideon left. In the last year, JJ had to go, even though she came back. Hotch was reassigned. You died, for crying out loud."
"I'm here now," Emily said with a sad face. "Reid, if I had any choice in the matter, I never would have left. I wouldn't have lied to you. I would have made sure you were the first to know I was okay…"
"But you still 'died', didn't you?"
They were looking at each other now. The painful silence now felt life threatening. It was the truth, she had let everyone think she was dead. But the truth was also that she wasn't the one to make the decision.
"I didn't run off on purpose. It just sort of happened that way," Emily said. "You know whose fault that was." Suddenly the anger Reid has for Emily was changing. He was becoming more angry with Doyle.
They both turned back to look at Doyle sitting in the other room. Reid's phone rang in his pocket.
"Yeah?" he answered. Prentiss continued to watch Doyle. Reid hung up the phone quickly, causing Emily to look at him. "Declan's disappeared. They had him at the warehouse but now they're gone." With that statement, and leaving Emily with a shocked face, Reid went into the interrogation room.
"Your ex is working with Laughlin McDermott." Reid was going to make this blatantly clear. When Doyle looked away, he continued. "How would he leave the country?"
Unhelpfully, Doyle spit out "I don't know. He's got endless funds. You'll never stop him."
"He hates you, doesn't he?"
"More than you do."
Reid had a moment of hesitation. With that line, he realized how close Doyle and Emily were, and how she might have said something about his past with her. Maybe Doyle knew more about the team than Reid thought. Reid recovered quickly.
"Then I think we should give him what he really wants," Reid said. He paused for effect. "You."
Emily burst into the room. "No. We are not letting him out of here, Reid."
"Emily, I will chain myself to him if I have to." That was his way of telling her, I still love you, but you have to let me do this one.
"He'll find a way to escape!"
"No he won't, and we're running out of time. If we find McDermott now we have a chance to save Declan." Reid knew that was why she did all of this in the first place. She didn't bother to argue with him further.
xXx
Getting into the helicopter, Reid and Prentiss sat on either side of Doyle. They had to be sure that he wasn't going to try to escape. It was silent for a long time on the way. Reid finally spoke.
"So how close were the two of you?"
Prentiss sighed and Doyle smirked. "You really never bothered to tell the boy about me?" The term 'boy' hurt Reid.
"He's not a boy. And why would I?" Emily was not happy. She didn't want to have this conversation with them.
"Because of how close we were." Doyle looked off in memory. Then he shook his head. "It doesn't matter anymore, I suppose."
"It does to me," Reid said.
"Why, Reid?" Emily said. "It was for my job. Look how well it turned out."
"I just wanted to know what I'm looking at." Reid was staring at the ground, since he couldn't look at Emily.
"Landing in under a minute," a voice said.
"Once we get there we're going to have to make the exchange." Emily sighed. "I'll take him out there."
"Not without me." Reid was determined. He was just having troubles, but he still loved her. He still wanted to know why she was with Doyle, but most of all he still wanted to protect her from anything that might happen again.
xXx
The gunshots went off. Doyle fell, Reid shot. He willed his eyes to stay open, but they didn't listen.
When they opened, everyone was on the ground. He ran to check McDermott's pulse, but found none. He looked over at Emily, who was holding Declan, but looking at Doyle.
Doyle knew he'd been shot, and that he was dying. He just looked at his son. He wanted that to be the last thing he looked at. He reached out a bloody hand towards Declan, who returned the gesture.
"I remember you," Declan said.
Doyle's face softened, like he could die peacefully. "Sorry, son."
Reid was to the side of Emily, but he could still see her face. Looking at her, he could tell that she was staring into Doyle's eyes, even if Doyle wasn't looking at her. Her face was sad. In that moment, Reid knew that she loved Doyle, at one point. A lot happened after her undercover work, but he knew someone couldn't hide those feelings. Maybe he'd show her that that was how he felt when he thought she'd died in that hospital.
xXx
Reid walked up to Emily. She had just announced to them over the round table that she was back, officially.
"I love that you're back." He said, simply looking at her.
"I love that you're still around," she said, smiling.
"I love that you two love each other!" Garcia squealed. She wrapped her arms around both of them. "I think it'll all be okay. If we give it some time."
The rest of the team laughed. "We all know it, too," JJ said. She stood next to Morgan, who was genuinely smiling since Emily came back. Rossi and Hotch, standing by themselves as the father figures, smiled in their approval of the ending result. The entire team was back together. And most importantly of all, Reid had Emily back.