This is going to be a mix of NCIS and eventually Rizzoli and Isles, but the main characters are Tony and Kate which is why I'm not submitting it as a Crossover. I hope you like it!
Tony Dinozzo sat alone in his living room eating the last slice of his pizza. Throwing the crust back in the box, he smiled at the satisfying 'thunk'. He looked around to see his apartment a mess. Blankets, pillows, magazines, DVD's, and cereal boxes laid around his living room. Gibbs had sent Tony home for two weeks after he had the plague and after a week, Tony was going stir-crazy. He missed the job and his team mates. He missed teasing McGee and his daily hugs from Abby. He missed hearing Ducky's stories; heck he missed Gibbs smacking his head whenever he made an obnoxious comment. But most of all, he missed Kate. He missed their bickering and arguing competitions and her smile and laugh... Boy, he missed her smile. It lit up her entire face and make her hazel eyes impossibly gorgeous. Tony laid back as he thought of his beautiful coworker. It wasn't right that he have thoughts about her like this. They were coworkers and partners and nothing more. Unfortunately... Tony took a huge gulp of beer to wash down that thought. Kate didn't even like him, not in that way at least. But she did stay with him when he was ill. That said something... right...?
Tony was deep in thought, considering what his feelings for Kate were when a knock on his door interrupted him. He stood up and picked popcorn out of his hair before going to answer the door. His heart jumped with excitement when he opened the door to see Kate Todd standing there smiling at him, holding Chinese food. "Kate! I'm so happy to see you! I'm so bored. I miss you guys!" he said excitedly as he moved aside to let her in. She stepped in and wrinkled her nose at the mess. "Wow, Tony. Martha Stewart you are not." she said as she smirked at him. "Yeah... sorry about the mess. I wasn't really expecting anyone. But if I knew I definitely would have cleaned up." he said as he quickly picked up the scattered blankets and magazines from the floor. He grabbed all the DVD's off the couch to make room for Kate to sit. She sat and observed Tony as he picked up the living room, placing everything in it's right spot. She began pulling out all the food setting it up on the coffee table. "You want a beer?" Tony asked her. "Sure." Kate replied. Tony disappeared into the kitchen and came back carrying two beers, hot sauce, and napkins. They settled down to eat and Tony asked her how things were at work. "Same old. Nothing truly exciting has happened. We investigated a petty officer who murdered his friend over a package of meth." Tony shook his head. "Yeah, nothing too interesting." Kate laughed and said, "So how are you holding up?" Tony groaned, "I'm dying here, Kate. I am bored out of my freaking mind! But Gibbs said he didn't want to see me for another week..." Kate smirked, "Poor baby... Well, I might make it more interesting for you." she said. Tony looked at her and saw her looking seriously at him. "Something tells me this is not a joking matter..." he said hesitantly. Kate set down her food and looked at directly at him. "You're right, this is serious. But first I need to ask you a question: How loyal are you to the team...?" Tony stared at Kate before answering her. "Very. I would lay down my life for any of you... why...?" Kate smiled sadly and asked her next question, "How loyal are you to me?" she asked quietly. Tony thought about the question very carefully before asking, "As a woman?" Kate shook her head. "As a friend. As a partner." Tony looked directly into her eyes as said confidently, "Very. I would die for you and I'd kill for you without thinking twice." They sat staring at each other for a couple minutes. Kate was stunned at Tony's response. She knew Tony was loyal to a fault but she had no idea that he felt that way for her. "Why are you asking me these questions?" he asked her quietly.
Kate took a deep breath before answering him. "Ari is back in the States." Tony's eyes got wide. "What? How? Does Gibbs know?" Kate shook her head and continued, " No, not yet and he is NOT to know yet." Tony was about to protest but Kate interrupted before he could talk. "Gibbs will know soon. Trust me. But for now this has to be kept quiet." Tony stared at Kate. "Why? What's going on?" he whispered. "I'm going into Witness Protection Program. A couple days ago, Fornell asked me to meet him for coffee. The FBI have tabs on Ari and inside information has confirmed that his target is me. Ari has to think that he killed me so he can report back to Eli David who is the director of Mossad, who will send his daughter, Ziva David to NCIS to take my spot. Also, you will be getting a new Director Jennifer Shepherd. It will be Director Shepherd's decision to have Ziva added to the team. Tony, listen to me: Ziva is working under Mossad. Her first mission will be to kill Ari in front of Gibbs: to eliminate Ari and earn Gibbs' trust . Killing two birds with one stone... But she has to stay at NCIS for several years earning everyone's trust. And you have to let her, Tony! Please, you have to let her in. You have to let her be part of the team. It's the only way this will work. I don't know what her complete mission is but I know it's going to take several years." She stopped for a minute to let all this information sink in. Tony was speechless as he listened to Kate. She was rattling off all this information as casual as if she was talking about the weather. "Say something..." she begged him. Tony shook his head, "And you're OK with all this? Leaving behind everyone and everything that defines you... for a job that you're not even going to be working anymore. And where are you going? What's going to happen to you?" "I know its a lot, but I love this country and I love you guys and I will do anything to keep you guys safe and to serve my country. I'm going to move to Boston and study to become a Medical Examiner. Later I will work for the Boston Police Department. My name will be Dr. Maura Isles. The only people who are to know that I was Kate Todd will be my mom, my sister, you, and Fornell." Tony stood up and began pacing the room. So many thoughts were running through his head. "Do you have any idea how the teams going to be after your death?" Kate closed her eyes as a silent tear rolled down her cheek. Tony sat down and softly brushed it away. "I know. Please give Abby so many hugs. She's going to be very upset. And don't tease McGee so much. He's a good Agent. And listen to Ducky's stories every now and then. And be the best Agent you can be for Gibbs. If I know Gibbs like I think I do, he's going to blame himself for my death." Tony hugged Kate and whispered a promise to her that he'll do anything she asks of him. "Am I allowed to talk to you and see you when you move to Boston?" he said. Kate nodded. "Yes, Fornell wants to talk to you sometime this week. He'll give you my new address and phone number when I get it. And we can still see each other and talk but it has to be discreet. No one from NCIS can know I'm alive. That's why I chose you to be the one at NCIS who will know I'm still alive. I really like you, Tony. You're a good person and I... I guess you could say I've had a crush on you ." she said shyly. "I didn't want to lose you. I couldn't leave you hurting like I know you would be if you believed I had really died." Tony took her hands in his and promised her, "I really like you too, Kate. And don't worry, you'll never lose me. I'll be in your life as long as you want." he kissed her forehead and pulled her into his chest. Kate lay there listening to his strong heart beat. She closed her eyes as she thought of all the people she was going to hurt when she 'died'. But she'll always have her Tony. Tony would be there with her every step of the way. So many thoughts were running through his head but he looked down at the beautiful brunette laying peacefully in his arms and knew he would give his best work in everything he did: in his life, his job, and this new relationship with Kate. He would do anything and everything to keep Kate and their team safe. He would give Kate everything he had. His heart, his soul, and if necessary his life. He tighten his arms around her as he closed his eyes and silently promised her his world. Together they fell asleep wrapped in each other's arms keeping their secret safe and protected from harm.