Disclaimer: I do not own SGA or the characters.

A/N: This is set after the series ended, but assumes the City got back home.

"Welcome back Colonel." A man smiled as John cracked his eyes open.

"Where am I?" The Colonel asked, not recognising the man talking to him.

"You don't recognise it?" The man questioned.

Attempting to sit up John scanned the room, which was similar to the Atlantis infirmary. The subtle differences were enough to make John tense as his mind ran wild going through the different possibilities from a bad dream to replicators.

"Your eyes don't lie. This is the Atlantis infirmary Colonel, albeit sporting a few changes from last time you saw it." The stranger said.

"Including you." John pointed out.

"Indeed. I apologise for not introducing myself. I am Dr Steven Doyle. I am the CMO."

"The CMO?" John asked sceptically. "Where's Keller?"

"Gone. As I said a lot has changed round here." The man explained. "Get some rest, everything will be explained when you are stronger."

John started to argue, only to find his eyelids getting heavy. Unable to stay conscious he fell back into darkness.

-00-

"You're awake." Doyle greeted. "I was beginning to get worried. How are you feeling?"

"Like I need answers." John replied tensely.

"Which you will get shortly." The doctor said. "But first I need to check you are fit enough."

"Fit enough?"

"Mentally and physically. I'm just going to run a couple more scans and then ask a few basic questions."

"Such as the location of Atlantis or my home world?" John asked convinced he was involved in an elaborate hoax.

"I assure you Colonel you are on Atlantis and we all know full well where Earth is. If you want I can give you the exact coordinates?"

"What I want is to understand what is going on and where Keller, McKay, Teyla and Ronon are." John said irritably.

"As soon as I have run these tests I'll take you to the briefing room where you'll get all the answers you need." Doyle replied. "So shall we start?"

"Fine."

"Full name and rank?" Doyle asked.

"Lieutenant Colonel John Sheppard."

"What's the date?"

"No idea. I don't know how long I was out for."

"Okay, what is the last thing you remember and what date did it occur?" Doyle rephrased.

"Everything is a little fuzzy." John confessed. "I was caught up in an explosion. I was trying to make it to a space gate. I lost control of the Jumper and got knocked out. Next thing I know I'm here."

"And the date that occurred?"

"August ish, twenty ten."

"Okay then. With time you should recover most of your memories. That's all I need from you. I'll just run the scans then take you to the briefing room."

"I know the way." John replied.

"I'm sure you do." Doyle smiled. "But my presence in the briefing has been requested."

-00-

John waited impatiently as Doyle ran his tests. With each passing minute he became more and more concerned that he saw no one he recognised in the infirmary. He was also confused by the uniforms that everyone was wearing. They were definitely not what he remembered. When Doyle finally returned John asked.

"What the hell is going on? Why don't I recognise anyone here and why are the uniforms different?"

"I promise a full explanation will be given." Doyle said. "All I'll say now is that some time has passed since you went missing."

"How much time?" John asked plucking a hair to see if it was still black.

"Colonel. You are going to have many questions, which I am not going to be able to answer. Dr McKay can. So I suggest that we go to the briefing."

"McKay?" John asked. "He's up there?"

"He is. So shall we?" Doyle asked.

"Sure." John agreed, not trusting the doctor, but impatient to see McKay.

"As I said," Doyle said as they walked down a corridor, "a few changes have happened round here."

"A few?" John questioned, noticing the different military uniforms, the changes in the corridor and the unfamiliar faces, who seemed to be staring at him. "How long exactly was I missing for?" The Colonel asked as they stepped into a transporter.

"Exactly?" Doyle asked. "I couldn't say. Although I'm sure McKay could tell you to five decimal places." The use of McKay's name once again helping to put John at ease. That was until they entered the control room and a silence swept over all the staff. Each person in the room staring at John wearing expressions of shock and awe.

"Why is every one staring at me?" John asked quietly.

"Your actions in your last battle saved hundreds if not thousands of lives. Everyone assumed you offered the ultimate sacrifice. No one here ever thought they'd see you." Doyle said climbing the steps next to John.

"So it worked? My plan?"

"To take out the armada?" Doyle questioned. "Yes it worked." He assured John as the door to the briefing room opened. As John entered he saw several strangers turn to face him before a man at the far end of the table stood and approached.

"Colonel Sheppard. It's an honour." The man said shaking John's hand. "I'm Matthew Finn, the leader of the Expedition."

"What happened to Woolsey?" John asked worried he couldn't see any of the team in the room.

"Please take a seat and we'll tell you everything." Finn said waving at an empty chair.

As John sat he asked. "Where's McKay?" Looking at Doyle he added. "You said he'd be here."

"He is." Doyle said calmly.

"No he's not." John said rescanning the room.

"Yes he is." Doyle assured him.

"No he's not." John countered.

"Yes I am." A man said.

Turning to face him John saw himself facing a stranger, who was somehow familiar.

"Colonel Sheppard." Finn said. "Meet Dr James McKay."

"Where's Rodney?"

"There's no easy way to tell you this." Finn said. "But he's dead. Everyone you knew is dead."

"What happened?"

"Time. You have been missing for over a hundred years."

-TBC