Found what I was looking for.

I own none of the characters here. just the plot. This is set just before Hiatus in season 3

Chapter 2

At that moment, everything went a bit crazy. Gibbs pinned Tobias up against the wall. "What on earth are you on about Fornell? You know Kelly is dead and you want me to relive that feeling."
"Believe me Jethro, I've spent all morning checking and rechecking this information." Tobias pushed Gibbs off of him. "Do you really think I would come here claiming that if I wasn't as sure as I could be."

The director stood, "Will you please explain what on earth is going on here Agent Fornell!"
"Yes please Tobias.." I asked him confused and still hurting from the earlier memory flash.

Tobias looked over at Abby, then to Gibbs, who nodded slightly. "In 1982, Jethro fathered a child with his first wife Shannon. Their daughter was called Kelly." The director went to say something but Gibbs gave her a look and she stopped.

"In '91 while serving in Kuwait, I got a message from back home, saying that Shan and Kel had been murdered in a car crash. I went to their funeral. It's why I became a NIS agent back in the day." Gibbs sat down, his face showing his pain. "Shan was testifying against a Mexican drug dealer, she had seen him kill a marine. He orchestrated the death of the agent protecting them. He died instantly. Shan and Kels died when the car crashed."

"Or so you were led to believe." Tobias adds. "I found this file deep in the FBI protection section. In '91 after the crash, Shannon and Kelly were airlifted straight to the closest hospital. Shannon had died instantly. Kelly was barely alive but the hospital managed to stabilise her. She spent a year in a medically induced coma and the director of the FBI decided to place her straight into protective custody. Having an FBI couple adopt her, they gave her a complete new identity."

"Why was I told she died? Why wasn't I allowed to raise my daughter?!" Gibbs snapped.

"It says in the file, Kelly was removed from Leroy Jethro Gibbs at the request of Joanne Fielding. Her maternal Grandmother, with the understanding that on her 18th birthday, Kelly would be told her life story and given the opportunity to find Jethro. Even Joanne doesn't know Kelly's whereabouts. At the age of 10, Kelly was renamed Amelia Addams and adopted by Agent Mark Addams and his wife Katie. The only people who knew that Amelia was Kelly were them and the director. Until I found out this morning."

"Joanne stopped me from raising my daughter?" Gibbs asked. Tobias nodded.

"Why wasn't I told this 5 years ago?" I asked.
"I don't know Mels. Like I say, I only found all this out this morning."

"How did you end up my daughter's Godfather?" Gibbs asked Tobias.
"I was best friends with Mark during FBI training. It's completely coincidental that I ended up her Godfather."
"This is unbelievable!" Gibbs snapped again and slammed the director's office door open and stormed out.

I finally found the strength to sit up more, I drew my knees to my chest. Not sure how to feel anymore.

Tobias stood between me and the door. Obviously unsure of whether to comfort me or to follow his close friend of years.

"Mels…" He said softly. I knew he wanted to follow his friend.
"Go. He obviously needs you. Just make sure you see me before you leave." I say softly.
"I'll stay with Miss Add…" The director reassured Tobias, pausing at my last name.
"Me too!" Abby says passionately.

"Thank you Mels. I'll be back, I promise." Tobias says and heads off quickly.

In the elevator. 3rd person p.o.v

Gibbs enters the elevator, quickly followed by Fornell. Gibbs slams the stop button so the men can have some privacy.
"So you are trying to tell me that… that girl up there is Kelly!" He says, devastated.
"I was coming to tell you when Jenny phoned asking for the next of kin for Mels." Fornell responded.

"And why are you down as her next of kin?"
"I can leave the office easier than Mark can."

"How did you find out all of this information?" Gibbs asked.
"There was a note on my desk this morning, asking me to go and find file 72 in the protection unit. I thought that was weird, file gathering is probie work. But I had nothing else to do, so I went and found it and it was labelled Gibbs. I couldn't help myself, I peaked. That's when I saw Kelly's name and I started reading more and checking facts within the report. I couldn't bring this to you without checking as much as I could first Jethro. The only other thing to do is a DNA test."
"Yes, Let's get Abby to fast track a test." Gibbs said, trying to finally calm down.

Fornell hit the elevator back on and the pair of them headed back up to the director's office.

Meanwhile, in the director's office.

Abby had sat next to Amelia while they were trying to make sense of what Tobias had informed everyone. "I don't understand why they wouldn't tell me?" Amelia whispered. "I've said to mum and dad multiple times that I was so desperate to find out where I came from. I just wanted to know where I had come from and what happened to me." Tears began to pool in Amelia's eyes which she wiped away viciously.

"Amelia. Gibbs is a very stoic man. I'm sure that all this will be very hard on him. I'm sure once he gets his head round all of this he will be back here. Ready to talk to you, work this out." Jenny said, moving closer to her two forensic scientists.
"I understand that Ma'am." Amelia said softly.
"Call me Jenny right now, Ma'am is far too formal for what we're discussing."

The two ladies smiled at each other.
The two men entered the office some moments later.

"Amelia." Gibbs started. The young girl looked up.
"Agent Gibbs." She replied.
"With your consent, I wish to run a DNA test for the pair of us. That's the only way we are both going to know the truth."
Amelia nodded. "That's fair Sir."

Abby jumped up and rushed to the door. "I'll go and get my kit."
"Thanks Abs." Gibbs said softly. "I'm sorry for rushing out." Gibbs added, looking at the young girl.
"It's ok. If this is the truth then I can totally see this being a big shock to you."

Abby reentered the office minutes later. "I'm here. Who's first?"

"I'll go first." Gibbs states, rolling his sleeve up. Abby makes quick work of entering the needle into Gibb's arm and retrieving enough blood for an accurate test. Once she had finished with Jethro, Abby turned to Amelia and repeated the process.

"I'll go and start running this. I'll get this done as quickly as possible." Abby said, disappearing to her lab.

"What do we do while we wait?" Amelia asked.
"We can start getting to know each other." Gibbs says softly.