Here's the next part for you, it might answer a few questions and raise a few more...
Present day. Miami:
He didn't understand. Why was Andy being so off with him? His last real memories were of the beating he suffered from the Malucci thugs, from then on everything was a blur. "Why are you looking at me like that, Andy?" he asked his voice still croaky from his brush with death.
It was one thing to find out that his friend was still alive but another entirely to believe that he had no memory of the things that he had done. "You and me," he began, "You think we can just pick up where we left off? You betrayed me, John." He turned away, unable to look at him anymore, the hurt evident in his voice.
"What? I don't understand?" Panic rose in him, the monitors attached to his chest registered his distress once more. "Andy, you're my partner. I'd never betray you." he tried to reason with his friend. Why was Andy treating him like this? They had always had each other's backs and he loved the man like a father, surely he knew that?
"You 'were' my partner," he spat; "Until you sold out to those bottom feeders." He gave his old partner a look of disgust.
"Who? I don't understand!" his voice rose as he struggled to process what was happening. He felt the walls of the room closing in on him. Three sets of eyes pinned him, his head pounded as he attempted to repair his fractured memory and place the fragments that remained in some kind of order. He looked desperately at Calleigh; she had been a port in this storm since he had woken up. Surely she would be able to make Andy understand?
She saw his agitation and reached a hand out to him, he grabbed hold of it as if it were a life line. "This is what Eric has been trying to tell you, he doesn't remember anything." she looked at Andy with pleading eyes, willing him to understand.
He wasn't sure what he felt any more, the last few days had been more than he could handle. Taking one last look at his old partner he shook his head and left the room telling them, "I need some air." At Calleigh's nod Eric ran after him.
She turned her attention back to Horatio, his breath coming in small gasps as he tried to hold back the tears. He looked over at her before squeezing his eyes shut; the events of the last 48 hours more than his damaged head could endure. The maelstrom of emotions that swirled within his mind was threatening to drown him; he could feel its pull dragging him deeper and deeper down. What if he never remembered? He realised that he would be left alone in a world that he didn't understand, with a partner who hated him and people he didn't know making attempts on his life. He had betrayed someone, of that he was sure but he refused to believe that he would ever do that to his partner. He felt the blissful cloud of darkness coming to envelop him once more, his mind attempting to shut off and protect itself. He slowly closed his eyes and drifted away.
He woke slowly, groaning as his body protested at the feeble movements he tried to make. Every inch of his body hurt, his arm felt numb as he tried to lift it towards his throbbing abdomen. After several tries his hand finally found the bandages as he rested it on top of his stomach as if holding the injured area would somehow lessen the pain he was in. He looked around the room and found he was alone, he remembered the faces of his friends and colleagues as they came to visit him over the last few days. "It must have been bad," he thought to himself as he remembered his ex-wife's tearful face when she came to see him.
He was lying as still as he could, even breathing hurt. He closed his eyes and willed his mind to block out the pain praying that a nurse would return soon to give him another shot of morphine. The sound of the door opening made him jump, he groaned as waves of pain cascaded through his battered body at the movement. "That looks like it hurts," an amused voice spoke from the doorway.
He opened his eyes and regarded the intruder, "Who the hell are you?" he growled, in no mood for pleasantries.
The man walked further into the room, "I'm your new best friend." he responded casually as he picked up the chart from the end of the bed and flicked through the pages absent-mindedly.
"What do you want?"
He put the chart back and walked across the room, closer to the bed. "It seems we have someone in common, Kelly."
His swollen eyes narrowed, "How do you know my name?"
"We've been watching you. You sure like to kick at a hornets nest, don't you?"
The pain wracking his body and the smug attitude of his visitor was beginning to frustrate him, "What are you talking about?" he said through gritted teeth.
"Word on the street is that you've been causing the Malucci brothers some problems. Poking your nose in where it doesn't belong."
"I'm a cop; it's my job to detect crime. It's what we do." he responded sarcastically as if he were speaking to a child.
The other man placed his hands in his pockets as he walked up and down the room, looking at the equipment. "And now you've got their attention. We've been trying for months to infiltrate them, and now you pop up. Perfect timing."
"Who is 'we'?" His visitor reached into his jacket pocket, for a moment he feared the man would shoot him. His eyes widened when he saw the badge the man had produced.
"Agent Collins, FBI," he said, before flipping the badge back over and replacing it in his jacket pocket. "You and I are going to work together."
"Says who?"
"Says the FBI. We've been watching the Malucci's for months, trying to find a way in. We had agents in the area when they attacked you; they heard what the muscle told you."
He couldn't believe it, they had heard what was happening and yet stood back and let him taking a kicking? "Thanks for coming to my rescue that night then."
His bitter tone didn't seem to affect the government agent, "It served a purpose, what would be the point of alerting them to our presence? Besides, we know they want you on their payroll."
He knew what Agent Collins was about to ask him, "No, I'm not doing it. I'd never sell out to a bunch of low rent bullies like them." He would have crossed his arms over his chest to emphasise the point but thought better of it with his damaged ribs.
"I'm not sure you're getting it, Detective Kelly," the other man said, his back turned towards the door. "You don't get a choice in this."
"Are you threatening me?" his gaze narrowed and zeroed in on the cocky agent.
"I don't need to threaten you; the Malucci's are doing a good enough job for me. You want to keep your ex-wife safe, your partner and that lovely woman you've been banging?"
He felt the anger surge through him, the thought of those he cared about being in danger infuriated him. "If I do what you ask, you'll protect them?"
Agent Collins turned to face him and looked him squarely in the eyes, "You have my word. We'll make sure that they're safe."
He took his time considering his answer, "I'll think about it." Not willing to give the other man an inch.
Agent Collins nodded and headed for the door, "I wouldn't leave it too long if I were you, you can't protect them all."