Disclaimer: I don't own Stargate Atlantis.

Note: This next chapter takes place in the future.

Seven years later (Seven Years 10 Months after Rising)

The Stargate activated.

"Unscheduled off-world activated"

Elizabeth left her office and went to Peter.

"Raise the shield."

A little boy with brown hair and brown eyes ran up to Elizabeth.

"Who is it Mummy?"

"I don't know honey."

Elizabeth turned to Peter.

"Do we have an IDC yet?"

Peter shook his head.

"Not yet, wait... receiving McKay's IDC."

"Drop the Shield."

The shield drop from around the event-horizon and McKay, Teyla, Ford and Sheppard step through followed by gunfire.

"Raise the shield"

Peter quickly raised the shield as Elizabeth rushed down the stairs to the team. Her attention went to John who was limping.

"What happened?"

"The villagers attacked us."

Elizabeth ran her fingers through hair.

"Briefing 20 minutes. Get down to the infirmary have Beckett check you out, especially you John, I don't want to skipping out on your check up again."

The little boy ran down the stairs towards the team.

"Daddy."

John picked him up and swung him around.

"There's my boy. You been good?"

The little boy nodded his head.

"Will you come play with me?"

"Sure"

Elizabeth took the boy from John's arms.

"After he's been to the infirmary Jonathan."

"Mummy," The boy cried

John took the boy in his arms again.

"C'mon, your Mum's right. I'll go to the infirmary, go to the briefing and then spend the rest of the day playing with you. Okay?

The little boy nodded his head and John set him back onto the ground.

The team made their way to the infirmary with Aiden and Rodney supporting John.

Jonathan clutched on to Elizabeth's hand.

"Is Daddy Okay?"

"He's fine. Why don't you up to Uncle Peter and ask him to play with you?"

"Okay"

Elizabeth watched as her son made his way up to Peter. She was aware that Jonathan knew that John wasn't his father. They'd told him when he was younger but it didn't seem to matter to him. Jonathan saw John as his father. Heck he was always there for him during every sickness, every nightmare, every birthday. Everybody on the base knew that John wasn't his father but they'd almost forgotten that in the past seven years. When they told Jonathan that John wasn't his father he got really confused and very upset and it would be a day she never forgot.

Flashback

2½ years ago

John and Elizabeth sat down with 'their' son.

"Sweetheart, we need to tell you something."

Jonathan was a typical four year old, unable to sit still, fussy and still tired from his nap.

"I want to play."

John pulled the boy onto his lap and kissed the top of his head.

"We'll go to play in a little bit, but first we need to talk."

The boy nodded. John had a way of calming Jonathan that continued impressed Elizabeth to no end.

Elizabeth started again.

"Honey, sweetheart, there's some...something that I...we need to tell you...I don't know how"

Jonathan looked at his confused mother; he was equally confused.

Elizabeth began to open her mouth too speak but John beat her too it.

"Okay I will tell you a little story. You know the story of how we came to be on Atlantis?"

The boy nodded his head; it was his favourite bedtime story.

"Well, before we came to Atlantis, we had lives back on Earth. I was a pilot and your Mum work in government; it's like what she does now only she advised leaders."

"It wasn't exactly like that, but it was close to it."

"Elizabeth."

"Sorry"

"Anyway me and your Mum didn't meet until she requested me to come to Atlantis, but you see at that point, when she asked me to come, she didn't know she was pregnant. With you."

It was Elizabeth's time to talk now.

"You see, back on Earth, I have a very good friend, a friend that I loved dearly. And because we loved each other so much, we made you."

Jonathan was in utter confusion. They were making this really difficult.

"Baby..." Elizabeth stood up "John I can't do this."

John nodded and looked at 'his' son

"What your mum is trying to say is that, I'm not your real father."

"Does that mean you don't love me?"

John quickly reacted to that. Jonathan was his whole world.

"No baby, I love you more then anything, don't ever think that I don't love you...

Do you remember when Uncle Rodney showed you all that stuff in that jar?"

The boy nodded, tears coming down his face.

"Well that was called DNA. It is material made up from two people or things to make one person or thing. Your DNA matches your Mum's in places but not mine."

Jonathan was getting more and more confused

"The fact is this, I am not your biological father, our DNA does not match. But, it doesn't mean that I love you any less. The first time I saw you, your mum had just crushed my hand and I was in a lot of pain; but when Uncle Carson put you in my arms, even though I was not your father, I loved you; and I will always love you."

"Does this mean I have two Daddies'?"

Elizabeth jumped in because John could not answer this question.

"No honey, it doesn't. This man here..." She pointed to John "...is your father. He has been with you since you were born, and even before then. Just because your DNA doesn't match doesn't mean that he isn't your father."

End of Flashback.

That had been 2½ years ago. As Jonathan got older, he'd asked McKay questions about DNA and genetics; but he never questioned who his father was. His father was John Sheppard and nothing could change that.

TBC...

I'm sorry, I don't know how you explain to a 4 year old that their father isn't really their father and I don't know how they'd react to news like that; but it was important for the next few chapters of the story. You'll see why of you keep on reading,

Anyway, hope it was okay and not to boring to read.