NCIS and SHIELD divided c1

What happens when Sam gets in trouble and asks NCIS for help? Will Ziva rejoin NCIS? What trouble will divide NCIS and SHIELD? Will they be able to work together to stop something terrible from happening? What secret is Sam keeping from Ellie will her family still accept her?

AN: So here is part two of my NCIS and SHIELD United series. I do not own any NCIS characters or Marvel characters. Tell me what you think by leaving a review.

CHAPTER 1

It had been 6 months since Sam and Bobbie had left after her family had been attacked. Ellie had returned to work in DC where she ended up spending time with Dalilah considering Tim and Tony were busy with Ziva catching up. Things had returned to a somewhat normal routine. They worked their cases thankfully nothing alien or abnormal. Ziva had moved in with Tony and it was official they were together. Ellie was worried for Sam but so far she has been keeping her word sending messages that she was alive if she did not ring. Ellie still had no idea where she was or what she was doing and in all honesty she did not really want to know.

"Grab your gear." Gibbs stated as he entered the ballpein as he grabbed his own things from his desk. Ellie, Tim and Tony jumped to it.

"Dead body?" Tony asked placing his gun on his hip.

"And Abduction." Gibbs stated leading them onto the elevator.

They arrived at the crime scene at a parking lot outside a cosco where Gibbs got right into it, he had Tony and Tim on witness statements as Gibbs made his way over to Petty Officer Michelle Fox wife of Lieutenant Matt Fox who was dead as Ducky and Palmer looked did their thing with Ellie next to them. It was their daughter that was taken and Gibbs was getting her statement. Things than moved at a very fast pace as child abductions go they knew they had a time limit. After getting statements and the crime scene was wrapped up they headed back to the Navy yard. Gibbs knew that solving his murder will help find the girl so he sent Bishop and Torez to Lieutenant Matt Fox's work where he was stationed talking to his work colleagues those who work under him and his CO. McGee was busy on the computer going through the Fox's life trying to find why their girl was taken. So far though everything was coming up clean.

"That was a total bust." Tony said returning with Ellie as he chucked his bag next to his desk.

"What?" McGee asked

"Nothing but good things about him, none of them could think of why this would happen to him." Tony replied

Ellie made herself comfy at her desk working on her computer on background checks of their friends to see if any might not actually like the Fox's but everything she was finding was that the couple were good to their friends.

"You have got to be kidding me," Ellie exclaimed in annoyance.

"You find something?"

"Only that I would have liked to be friends with the Fox's I went searching their friends posts and nothing but good things I mean they never missed a birthday, or major event in any of their friends lives. It seriously makes them look like the perfect couple." Ellie said

"Doesn't help us find the girl." Tony said

"I know that Tony."

"Where is Gibbs?" Ellie asked seeming they haven't seen him all afternoon.

"Either getting coffee or working on his boat. He had this look when he left. Been waiting for a call." McGee replied knowing that look that usually meant give him time and he will have it.

"I might go check on Abbey." Ellie said

"I will check on Ducky." Tony said as he was also hitting a stone wall. Tim was still busy going through their past and online activity.

The next day Gibbs entered the ballpein to find Ellie and McGee asleep at their desks he couldn't see Tony anywhere he placed the coffee and burrito in front of Bishop and she woke up instantly her eyes zeroed in on the burrito picking it up and began eating it as Gibbs went over to Tim and did the same but he did not wake up so Gibbs stood there staring at him as if he could will him awake.

"Yes Captain America..." Tim said sitting up at attention he had to blink a couple of times to focus before shaking his head. "Sorry boss."

"You dream of Captain America?" Tony asked he was standing behind Tim's desk.

"What? No! How?"

"Abbey found something." Tony said so Gibbs left to follow him down to Abbeys lab.

"Gibbs you're here. Okay stand here and watch this." She said showing a video of a family.

"Why am I watching this?" Gibbs asked

"This is the real Matt and Michelle Fox."

"Then who the hell is in the morgue and who have we been talking too?" Gibbs demanded

"I don't know, but it is a really good cover. I mean I wouldn't have found this if it weren't for Bishop going through the friends this is them out of high school. High school sweethearts can you believe that? Would have missed it too if it weren't for McGee's facial reconstruction app. The faces don't match up.

"DiNozzo."

"Go pick up fake Mrs Fox on it." Tony said heading out.

"Good job Abs." Gibbs said placing a caf-pow in front of her before following after Tony.

They drove to the house before entering surprised that she was still there.

"Petty Officer Fox, we would like you to come with us."

"Have you found my daughter?" She asked

"Come with us, we have some questions." Tony stated

"I only have one, have you found my daughter?" She asked

"What is your real name?" Gibbs asked back knowing she would not go back to NCIS he decided to talk to her there.

"What?" She asked surprised

"We know you are not Michelle Fox or your husbands name was Matt. It is a very good cover we almost believed it. Almost." Gibbs stated and watched as the woman before him swallowed and looked down.

"I need to make a phone call." She said

"Not until you start talking." Gibbs pointed

"Please I will make the call and all will be explained." She said

"You're in the witness protection program?" Gibbs realized "Who were you running from?"

"Oh god, please no." She said dialing her phone she stated something and waited she agreed and hung up. She did end up going to NCIS where they were met by two federal marshals.

After being briefed they started a man hunt for Gregor Green. They were four hours in when Michelle's phone went off.

"Hello?"

"Mummy?"

"Jasmine? Where are you baby?"

"Apartment c5 room 34 on Dunstun street."

"Is there anyone with you?"

"The bad men are sleeping." Jasmine said

"Sleeping?"

"That's why the lady said."

"What lady?"

"The one from the window. She made the bad men sleep and gave me the phone to call you."

"Is she there?"

"No she went out the window again."

"Alright Jasmine we are coming. I am coming baby." Michelle said as they were in the car and on the way.

Gibbs made Michelle wait out with the marshals as he went in with his team with guns drawn. They passed several men all of them unconscious. When they made it into apartment c5 room 34, here they could see a fight took place there were bullet holes in the walls and most of the furniture was smashed. They searched the place securing all the men.

"Jasmine?" Ellie called out and they heard a small noise from a wardrobe. Ellie got down to her level getting her to come to her.

"Are you agent Gibbs?" Jasmine asked stopping in front of him.

"Yes."

"Here, she said to give you this. She said it will help." Jasmine said giving him a USB stick where he took it kneeling down next to her.

"You are very brave." He said to which she smiled up at him before Ellie took her down to her mother.

"McGee." Gibbs said handing him the stick as he turned to him. Before looking around the room, McGee moved over to the computer on the table surprisingly not damaged. He scanned through its content once he hacked it unlocked.

"Found the entry point, the kid was right, whomever knocked those guys out entered through the window. The building next door. "There is no ropes." He added as he started taking photos. "Not even bloody glass. Whomever it was is a pro." Tony remarked and Gibbs had to agree.

"Well we might have them on camera." Tim stated as he brought it up on the computer. Gibbs looked over his shoulder as Tim brought it up they saw the window smash but then the cameras all went dark.

"McGee?"

"They knew what they were doing." Tim said

"Start processing." Gibbs instructed. They spent the afternoon processing the apartment those unconscious were taken to be held. Gibbs only claimed the one that was in charge Gregor Green's second in command he was planning on interrogating him, himself. They found that most of the others were hired guns. They remained silent not giving anything. So Gibbs called it for the night sending his agents home seeming they had gotten Matt's killer and Jasmine's abductors.

Gibbs headed home when he got to the door he saw the lights on in his house so dropped entered his home with gun drawn only to freeze in his living room as he saw who had broken into his home.

"What are you doing here?" Gibbs asked lowering his gun.

"I needed a place to lay low for a while...couldn't go to Ellie's they will be watching her place."

"Who?"

"SHIELD. I screwed up Gibbs I need your help." Sam Bishop said looking up at him from his couch as she sat up she winced and only now did he note the blood on her shirt.

"Are you hurt?" Gibbs asked even though it was obvious she was.

"This? Just a scratch." Sam said as Gibbs moved forward to apply some pressure to the large gash on her side giving him time to examine it.

"This will need stitches." He said "Where is your soulmate?"

"We had a fight." Sam shrugged as Gibbs left to get some medical supplies when he returned.

"I am calling Ducky." He said grabbing his phone noticing that she was rather pale and sweaty.

"Don't tell him I am here. Ask him to come over but you can't tell anyone I am here. Not over the phones." Sam said and Gibbs knew she was not being paranoid.

15minutes later Ducky arrives and when he sees her he reprimanded her telling her she should be at a hospital.

"Sorry doctor, no hospitals." Sam said as Ducky stitched her up.

"What sort of trouble are you in that you can't go back to your organization?" Gibbs asked

"I didn't do what they think I did."

"What do they think you did?"

"We were overseas, on a mission and things went south. Something…happened and I solved it. I thought I was doing the right thing…turns out not quite right. But in doing so I left my post and somethings went down now I am in trouble for something I didn't do I swear Gibbs I did not do it."

"What? What do they think you did?" Gibbs asked again as that was very vague and he had no idea what she was talking about.

"Some kids got hurt, I moved to help them and it went missing."

"They think you took it?"

"Yeah."

"How can I help you?"

"I don't know, I just need time to prove that it was not me. I need to find out who did it and where it is."

"What about agent Hill?"

"Kind of not on speaking terms with her. I left before I could be debriefed. They currently think I am rogue. Which is technically true but…I don't know what to do." Sam said getting up she began to pace. Gibbs shared a look with Ducky who was sitting on his other couch. There was a knock at his door so Gibbs sent Sam down to the basement as he went to answer it.

"Bishop?" he asked seeing her standing there she looked upset.

"Something bad has happened to Sam."

"OH?" he asked moving aside letting her into his house.

"Yes, I had a call from Maria and a visit from Bobbie both of them can't get in contact with Sam. They are looking for her, I need to find her if something has happened to her…" Ellie said as Gibbs led her down the stairs to his basement after getting her to leave her phone on the table.

"I have to ask, how do you get the boat out of here?" Sam said looking at Gibbs only to freeze at who was walking behind him. "Hey El?"

"Seriously? That is what you say, I just had a very interesting conversation with Maria and Bobbie. They are worried about you."

"You can't tell them you have seen me."

"Sam what is going on?"

"I have to go, no doubt you were followed."

"What? Sam talk to me please."

"If you want our help."

"It was a mistake coming here. Thank you doctor for the stitch up…I need to get going."

"No, you can stay here for the night. We will help you in the morning. Ellie and Ducky will leave if they are watching the house you can't leave. Ellie will have to act that she has not seen her sister and tomorrow we will get the others on board. We will help anyway we can." Gibbs said making Sam look at him, she was surprised he was helping her.

"You went out of your way to help Timothy, and are Eleanor's sister we will help you." Ducky said Sam could only smile at the help they were offering.