This is based on the following spoilers:
Taking things further with Tony and Ziva.
Big revelation for Ziva mid-season.
Fallen heroes theme (not that I've ever consider Eli David a hero)

Tony had been starring at Ziva's desk for the past few hours. Where could she possibly have gone? He had left to get some pizza and McGee had been in the lab with Abby. When they had returned she was gone. Gibbs was defiantly going to get pissed about it. The case may be closed, but the reports don't write themselves. And just as he finished that thought Gibbs came walking into the bullpen.

"Where is David?" Gibbs looked at the empty desk beside him.

"I sent her home."Vance entered the bullpen."I've put her on 2 weeks personal leave."

"Why?" Tony asked.

"Eli David was found dead this morning."

The 3 men fell completely silent.

"What happened?" Gibbs asked.

"The doctors said that it was a stroke. But according to his medical records, he has been sick with lung cancer for the past 2 years."

"Did she know?" McGee blurted out.

"No, she didn't."

Tony and Gibbs shared a look, both obviously worried about how Ziva's reaction to those news. Eli David might have been many other things but a good man, but he was still Ziva's father and the only member of her biological family she had left. Now he was gone too. And she hadn't been able to fully make peace with him. Gibbs and Tony thought the exact same things. Gibbs then nodded to Tony. And that was all Tony needed as permission to get his things, walk to the elevator and drive to Ziva's apartment.

"Ziva?"Tony said as he gently knocked on the door."It's me."

He then heard her move around inside the apartment. The shift of her weight as she got up from the sofa and walked towards the front door. He knew exactly what he would see. Ziva, his partner of almost 7 years, with her walls rebuild. She would try to look brave. But she was no longer able to hide the red eyes and sad expression from him. And when she opened the door, his mind immediately went back to the events a little over a year and a half ago. When Mike Franks had just died and Ziva let him see her cry for the first time. The first time she didn't try to hide it. And she had let him comfort her. He just hoped she would let him do it again.
Ziva was still wearing the clothes she had been in all day. Her hair was in a messy bun and her eyes were clearly red from crying. She only shot him one look and then she returned to her spot on the sofa.
Tony didn't question her. He just closed the door behind him and sat down next to her on the sofa. They sat like that for a while. He wanted her to decide if she wanted to speak to him. Maybe she just needed him to be there, and not say anything. But then she spoke.

"I wish he had told me."

"Maybe he didn't want you to make peace with him for that reason."

"Maybe."Ziva sighed."I got an email from him 2 weeks ago. It was the last time I spoke to him."

"What did he write?"

"That he hoped I was happy. That it was all that mattered to him."

Tony then noticed there was a picture on the coffee table. Ziva noticed him looking at it. She reached for it and held it for him to see.
It was a family picture. Ziva looked about 4 years old, standing next to Ari at a small coffee table in a garden. Eli stood next to Rivka who sat on a small chair with baby Tali on er lap. They all looked happy.

"They are all gone now."Ziva looked down."I cannot stand to lose anymore."

He offered her a comforting smile and reached out his arm. She leaned into his chest and rested her head on his shoulder.

"I'll never leave you Ziva."He said."You'll always have me."

He caressed her arm gently and looked down at her. He couldn't see her face but he knew that she had closed her eyes.

"I know." She whispered peacefully.