I watched Aliyah last night and came up with this in my head. This is how I'd wished it had gone.

“You jeopardised your entire career and for what?” Ziva snarled.
“For you.” He said it so softly she almost wasn't sure if he had said it.
Her right hand swung up, to punch him no doubt (frankly, he didn't blame her, he'd already punched himself twice) but he was prepared and caught her wrist before it made contact with his face. Her other hand barely came up before he'd grabbed that wrist also. Without thinking, he pushed her around a column and into a corner. Ziva tried to wiggle her way out of her grip, but he saw that coming, and planted his hand just above her head, her wrists still trapped.
“Let go of me, Tony.” Ziva hissed.
“I'm not scared of you, Ziva.” Tony said softly. “I don't care if you're going to kill me, you have to at least hear me out.” Ziva stopped struggling and looked at him, anger still flashing in her eyes. So Tony continued.
“Rivkin was using you.” Tony said softly. “In two ways. One, your father was beginning to doubt your loyalty to Mossad and sent Rivkin to seduce you and bring you back. Two, he needed an excuse to remain in DC. He was trying to find a terrorist's training camp and the camp had links in L.A. And DC.”
“How do you know this?” Ziva snapped.
“Someone's coming.” Tony pulled her further into their corner, just enough to melt into the shadows. He no longer could see her expression but knew it was not good.
“How do you know this, Tony?” she repeated. “Did you get it from the cow's mouth?”
“It's horse's mouth, Ziva, and yes I did.”
“How could you have?” Ziva snarled.
“I was having a conversation with Vance and her forgot to hit the end button before he had his special meeting with your father.” At that, Ziva froze.
“My father and Vance?” she said with outrage. “They're working together?”
“I don't... actually know.” Tony confessed. “That's the vibe I picked up.”
Her eyes narrowed into slits. “I can no longer trust you. How do I know you are telling the truth?”
“Ziva, you trusted me before this. Why don't you trust me any more?” Tony's voice was hurt, and he didn't even try to hide it.
“I- I- You killed Rivkin!”
“Are you angry because I killed a fellow Mossad officer or the man you loved?”
“That is not an important question!”
“It is to me!” Tony said, his voice lifting slightly. Ziva watched him carefully. He sighed. “Where do your allegiances lie, Ziva? I will not leave until I have an answer. Who do you trust, NCIS or Mossad?”
“Tony, I do not trust you! You killed Michael Rivkin!”
“That shard of glass in his side? He was coming at me with it. I killed him out of self defence.”
“How can I believe you?” she asked.
“Am I the kind of person that would lie to you to save my own ass?” Tony's words caught her by surprise. “Ziva, I went there to talk to you. We found records on Abin's laptop that proved his laptop had been connected to your network. I was going there to speak with you about it, but when Rivkin...” He trailed off.
“He was drunk.” Ziva snarled. “You should be dead.”
“But I'm not.” Tony said. “I will ask you again. Am I the kind of person who would lie to save my own ass?”
She looked up at him. “No.” she said softly.
“Did you ever truly trust me?”
She hesitated. Never a good sign. “Yes.” she finally said.
“Do you still trust me?”
“No.” That was a given. He sighed.
“Will you ever again?”
She wanted to come up with a smart remark, but she answered almost immediately, “Yes.”
“How? I can never regain your trust.” Tony knew this for a fact. Gaining Ziva's trust was like building a reputation. Takes years to build, seconds to destroy.
“You have one chance.” Ziva said softly. “You don't have to do a thing. I will find out for myself whether or not you are telling the truth.”
“All right, but do it fast.” He released her wrists and watched her go.

Okay, a couple thing here. First, when I first wrote this, I forgot Tony had a fractured radius and wrote it as if both hands were free. Oops. Two, I forgot the name of the man who committed suicide- something like Abin- and I couldn't find it anyhere online, so... yeah. Third, I'm pretty sure this will be written in four parts, and I will NOT be continuing, because then I'd have to rewrite Season 7 and I really don't have the time to do that. Okay, this was one long footnote. I'll just go and... crash into a wall.