Note: This is for Susn, who requested this fic right after The Return aired (bless her patience) and actually outlined much of the plot. Susn, I'm sorry it took so long and I hope it lives up to your expectations. Although I have several chapters rough drafted, it isn't finished yet. I'll try to keep updates frequent, but I'm working off my work computer, which is somewhat limiting. I really wanted to get this going before the "real" part 2 aired in the US (I have no idea why).

Summary/Spoilers: This is an AU tag or part 2 of The Return, so obviously many spoilers for Part I of The Return. This is our version of what happened when the puddle jumper with our team went through the wormhole to an Asuran controlled Atlantis. There is a large focus on the connection between John and Atlantis, because we love that and always yearn for more.

Disclaimer: I do not own Stargate Atlantis or have any rights to the show or the characters.

The Return Part 2: Favorite Son - Chapter 1

As soon as the jumper burst through the gate into Atlantis, they were under fire, bursts of light flashing as the shots hit the shield.

"I need the door open, Rodney, now!" yelled John.

"Just move, I'll have it open when we get there," Rodney yelled back, his fingers working furiously on the keys of the computer.

John responded by moving the jumper up toward the jumper bay, the doors pulling open just as they arrived at the ceiling of the gateroom. The shots diminished as they rose through the jumper bay and toward the now opening roof. A minute later, they cleared the city and took off across the sky. Drones immediately came after them, forcing John to swing the spacecraft first one way and then the other as he took evasive maneuvers.

"I think they're getting closer. Are you sure about this plan of yours?" Rodney hung onto the armrests of the chair, his eyes wide as the ship turned almost on its side.

"Not now, Rodney," said John, focusing all his thoughts on evading the drones seeking to destroy them. One passed by close enough to clip the back edge of the jumper, shaking it roughly. "All right, now I'm really pissed," he muttered, taking the jumper down. "Hang on, we're going in," he warned just before the nose of the ship entered the dark waters surrounding Atlantis.

In contrast to Sheppard's warning, the entry was relatively smooth, more so than his passengers had expected. Rodney's grip on the seat tightened, a move not lost on his friends. A firm hand appeared on his shoulder, startling him until he looked back to see Teyla's comforting smile.

"It is all right, Rodney. We will be fine."

Rodney nodded, trying to seem more confident than he felt. "Yeah, I know. We aren't going very deep, right?"

"Not this time," said John. He made his way through the water, hoping Rodney's jamming device was successfully keeping the Asurans from tracking them for at least a few minutes. That was all he would need.

After several minutes, the ship eased out of the water and slowly set down on a dark pier. "You realize we're on the far side of the city and it's quite a walk to free O'Neill and the Ancients, assuming they're still alive," pointed out Rodney as Sheppard powered down the jumper.

"I know."

"You also know that this part of the city was heavily damaged in the storm and is likely to be unstable,."

John nodded and grinned. "And you will notice that because of that damage and distance, that this part of the city hasn't been repaired and powered up, making it unlikely that there are any working sensors to detect us."

Rodney looked out the window at the dark structures rising before them. "Oh, I knew that. I was just making sure we were on the same track."

John grunted and slapped Rodney on the shoulder as he stood up. "Sure, Rodney." He made his way to the back of the jumper where his team was gathering up their equipment. "Everyone knows the plan, right?"

Nods came from everyone, including Rodney, who had joined them in the cargo bay. "We're ready, colonel," he said, trying to sound more confident than he felt.

"Good. Let's get our people and take back our city." John lowered the hatch and led the way out. When everyone was on the pier, he raised the hatch and cloaked the jumper. "Okay, let's remember where we parked," he said, trying not to dwell on the disaster that had occurred the last time he'd used that phrase.

They carefully made their way through the darkened hallways, slowly closing the distance between them and the holding cells. They were hoping if any humans or Ancients had been taken alive, that they would be in the cells previously used by the expedition to house Wraith prisoners. Their movements became more careful as they entered the functioning part of the city, where the corridors were lighter and they were more likely to find unwelcome company.

John ran his hand along the wall, feeling the familiar hum of his city. I'm back, he told her with his thoughts. He was surprised at the swell of emotion that rushed through him and wondered if it was him or Atlantis or maybe both. He could feel her welcome him and the rush made him momentarily dizzy. Pausing, he leaned against the wall, grinning as the emptiness he'd felt these past few weeks filled. At least now he understood.

"Colonel?"

John looked up at Beckett's whisper, reading the concern on his face. "Sorry, I'm okay. Atlantis is just glad to see us."

Rodney snorted softly. "You mean she's glad to see you. Her favorite son has come home to her."

John grinned, undisturbed by Rodney's slightly biting tone. "You're just jealous because she likes me best." He rubbed the wall affectionately. "I'm glad to see you too, girl. Now we have to rescue you from the evil Replicators." Keep us hidden as long as you can, he thought.

Rodney rolled his eyes. "Could we get on with this already, you know, before they discover us and make us die some kind of horrible and painful death?"

John grinned and nodded. "Let's go."

Elizabeth and Carson exchanged a glance, both resisting the urge to roll their eyes at the two juvenile acting adults in front of them. A few minutes later, they arrived at the door leading to the cells, surprised to find no guards in the hall.

John turned to his team. "I'll take point and Ronon, you're right behind me. The rest of you wait until we've cleared it." He turned and paused by he door, waiting on Ronon to get in position right behind him. At the big man's nod, he opened the door and dashed in low, moving quickly to his right. Ronon followed his moves, but went left. Both of them scanned the room, squatted low with their guns up and ready. John was peripherally aware of movement behind the bars, but the rest of the room was empty.

"Colonel Sheppard, is that you?"

John stood up and watched as General O'Neill made his way to the front of the cell. He gave a quick nod to Ronon before walking over to stand in front of the prisoners. "Yes, sir, General. We've come to get you out of there and take back our city."

O'Neill grimaced. "I know I'm going out on a limb here, but I'm guessing General Landry didn't exactly approve this mission."

John shrugged his shoulders noncommittally. "Not exactly, sir. He said something along the lines of taking care of my military future, but I didn't hear exactly what he had in mind. Nothing good, I'm sure. I believe his plan was to blow up the city. We . . . had a little problem with that."

"He wanted to what?" asked Helia, moving up to stand beside the general. "This isn't his city to blow up."

"That's kind of what we thought," said Elizabeth as the rest of the team entered the room.

"That, and we don't leave our people behind. Not even generals, sir," quipped John.

O'Neill quirked one side of his mouth as he bobbed his head once. "It's not that I'm not grateful, because I am, but do you have any idea how you're going to pull this thing off? You may not have noticed, but the Asurans aren't exactly a friendly bunch."

John nodded toward Rodney, who had already disassembled the control panel to the cell door and was working on it. "Step one is to get all of you out of there and I brought a genius with me who just happens to be well-versed on Ancient technology."

Rodney raised one hand without looking up and then continued to work. John exchanged a smile with Elizabeth and Carson.

"Nice, Colonel, but I'm in the company of several individuals who just happen to be living, breathing Ancients and they couldn't get us out."

"If you'll excuse my saying sir, they are inside the cell whereas we are outside the cell. That gives us a bit of an advantage."

O'Neill looked slightly taken aback. "Oh, yeah, I should have thought of that. Must be something about having Replicator hands stuck in my head."

John winced in sympathy, the feeling all too familiar and recent. "I know what you mean, sir. Not a pleasant experience at all."

"Only if you enjoy having your brains scrambled and then turned inside out," murmured O'Neill. "Personally, I'm not a fan, but that could just be me."

"Got it," said Rodney as the shield deactivated and the door opened. He stood back away from the door, grinning proudly.

"This seems too easy to me," said John cautiously.

Rodney's face fell. "Easy? What are you calling easy?"

"Where are the guards?" asked Ronon, his tone and expression showing his support of John's statement.

"They did not feel the need for guards. They are arrogant and have underestimated their enemy," announced Helia. "As I am afraid we have been. We foolishly believed we could not be bested and yet we very quickly were. I will not make that mistake again. Do they know of your presence?"

John nodded. "They know we're around, but they don't know we're in the city yet."

Helia frowned. "They must know you are here. Sensors are active in this section."

John shook his head. "Atlantis can hide us for a while, but we need to get moving. She can only help us so long before the Asurans figure it out."

Helia frowned up at John. "I don't understand, how is this possible?"

Rodney grimaced and sighed. "Because she likes the Colonel, a whole lot. This isn't the first time she's hid his life signs to keep him from being found. He's her favorite you know."

"No, that is not possible. The city is not capable of communicating with an individual on that level." Helia's expression and tone of voice was decidedly skeptical.

"Well, say what you will, but she always responds to gene boy over there like no one else. She'll sing for him and barely hums for the rest of us," said Rodney.

"As much as I'd like to hear about your love connection with the city, I think I'd rather hear about this wonderful plan to save our collective hides about now," said O'Neill. "What did you have in mind?"

John nodded, switching back into military mode. "I'll take Rodney and Elizabeth to the chair room to launch an attack on the Asuran ship in orbit. Ronon, Carson, and Teyla can take the rest of you to spread out and handle the ones in Atlantis. We brought all the anti-Replicator weapons we could get our hands on. You and Mr. Woolsey can go with whatever group you want to and," he turned to Helia, "I'm sure you'll want to decide what your people do."

Helia nodded. "Dolon and I will accompany you to the chair room, as he is our expert on chair operations. The rest can help your people with the forces in the city." She turned to a tall, slender man at her side. "Savill, you will coordinate our forces with Ronon."

The blonde man nodded, determination in his expression as he pursed his lips together.

John nodded at the Ancients. "Is this everyone?"

"No, there are others in the cell adjacent to this one," said Savill.

Rodney grabbed his equipment. "I'm on it," he said as he left the room, one of the Ancients hurrying along behind him.

"The thing is, we have to try and hit them all at once. Our weapons will disrupt them, but after some of them have been hit, the others start to figure out the frequency of the energy burst and adjust to it. We need to try and take them all out in as short a period of time as possible." He saw the general nodding, experience clouding his eyes. "And if we start the chair operations too early –"

"They will shut you down," finished Helia.

"Right," said John. "Atlantis can only shield us for so long and not when we activate the chair. It draws too much power."

Helia narrowed her eyes at him, frowning slightly. "I still don't understand about Atlantis shielding you. If we manage to survive this, we need to talk."

John grinned mischievously. "How about if I tell you a few things about your city and you let me and my team stay around? We've grown rather fond of Atlantis."

Helia cracked a small smile. "If you can truly return control of the city to us, then I will consider it. Perhaps you would be valuable allies after all."

"So, Colonel, are you going to stand around all day flirting with the nearest Ancient woman or are we going to take the city back?" Rodney asked from the doorway.

"We're taking our city back," John said confidently. "General, what do you and Mr. Woolsey want to do?"

O'Neill glanced briefly at Woolsey before looking back at Sheppard. "Give me one of the weapons and I'm going with Ronon. I'd like nothing better than to kick a little replicator ass right now. I think I owe them a thing or three. You'd better take Woolsey with you, though. I don't think he's exactly ready for the front lines just yet."

John nodded, noting the disheveled and frightened man in a suit. "Yes, sir. We'll take good care of him." He turned to his team. "Move out, radio silence until we're in place."

John was disappointed, but not surprised when they arrived at the chair room fifteen minutes later to find it guarded.

"What do we do now?" whispered Rodney as they crouched in the hallway.

John closed his eyes a second, focusing on Atlantis. Abruptly opening them again, he motioned down the corridor, back the way they had come. The team very quietly made their way down the hall until they could duck down a dark side corridor.

"What now, John?" asked Elizabeth. "Can we take them?"

"We could take them, but then the Asurans would know for sure we're here and that would give them time to start adjusting to the weapons. We can't take that chance."

"We could wait to take them until Ronon and the others start their attack," suggested Rodney.

"No, then the ship would have too much warning before I could get drones off. There's another chair that can be brought online and activated. Atlantis can help us override this one so that we can attack the ship at the same time as we attack the Asurans in the city."

Helia frowned and stepped forward. "There is another chair, but it is in the damaged part of the city. We haven't even restored power to that section yet because it's so unstable. How did you know it was there and how do you know it can be used to override this one?"

John grinned. "Atlantis. We told you, she likes me. Come on, we have a stop to make first and it will take several minutes to get there, even if we hurry."

Rodney smirked at Helia as he hurried past, taking in her confused expression. "When it comes to Atlantis, you really do want to be on his side." He rushed down the corridor, followed by the rest of the team and the two Ancients.

oOo

Ronon peered around the corner and quickly pulled his head back. He smiled and nodded to Teyla and then back toward the corner, holding up all five fingers on his left hand. She acknowledged his message with her own slight nod. Teyla turned and slipped down to the end of the hall where General O'Neill waited with three Ancients.

"Ronon has five at this corridor. I will stay and assist him, as there may be others farther down that we cannot see."

O'Neill nodded. "Good. I'll take our new friends the rest of the way to the control room. With us on this end and that . . . Idiot guy on the other, we should be able to get them all."

Teyla raised one eyebrow at him in dismay. "I believe his name was Idaeus."

O'Neill looked slightly flustered as he moved his mouth a few times before getting sound to come out. "Okay, whatever. Why can't they have simple names like Bob or Harry or Tim?"

Teyla's expression sharpened. "Perhaps they find your names to be odd and hard to remember as well."

O'Neill looked at her for a few seconds and then cleared his throat. "I'm guessing we should get to our post now. Good luck."

Teyla smiled and nodded as she watched the general motion to the Ancients with him and hurry down the hall. She found him to be a strange man, but then she still found Sheppard and McKay to be strange as well most of the time. Must be something about Earth men. She steeled herself for the battle soon to come as she made her way back to Ronon.

oOo

John led the way into one of the power control rooms at the outer edge of the inhabited portion of Atlantis. "Rodney, I need you to divert some power." John touched the panel and brought up a map of that section of the city. He looked at it for just a second before pointing. "Here. We need power diverted to this room, enough to activate a chair."

Rodney looked at the schematics and then pushed a few panels. "Maybe . . . I can get you power, but I'm not sure if I can get you enough."

"Do what you can Rodney," said John, watching the scientist work.

Dolon stepped up to the console beside Rodney. "I can help. I'll get the main routing converted and you carry it to the second chair."

Rodney nodded as he continued to press panels. "Yes, yes, that should work."

Less than five minutes later, Rodney pulled his hands back, nodded to Dolon, and turned to face John.

"You have power, but I'm not sure if it will be enough."

John nodded and put his hand on the panel for a few seconds. "We can make it work. Good job, guys. Let's go, we don't have much time."

They hurried out the door and down the corridor, not bothering to be as quiet as before since they were in the damaged outskirts of the city. The halls were dark and debris littered the floor, making the going rough in places. A few minutes after leaving the power control room, John rounded the corner to come face to face with an Asuran. Acting on reflex, he immediately tackled the man, knocking them both to the floor. His head connected with something hard and his vision darkened.

"John, come on and get up, we have to go."

The muddled sounds that had been scrambling around in his head finally clarified into the voice of Elizabeth. His vision finally decided to focus a second later to find her face near his.

"John, are you okay?"

The pilot immediately began sitting up, the urgency of the situation flooding his thoughts. "Yeah, sorry, guess I hit him a little harder than I intended." His head swam for a second before he made out the pile of metal cubes on the floor next to him.

Elizabeth's face was grim. "We had to shoot him."

"Crap! We'd better get moving. They know we're here now." John used the wall and Elizabeth's arm for leverage so he could get to his feet. The hall swayed for a second, but thankfully settled down fairly quickly. John hurried down the hall and around the corner. They were almost there.

"Sheppard, this is O'Neill. We're in position," came the barely audible whispered voice.

Just as quietly, John responded while entering a room and making his way to the chair in the middle. "Give us a second, we had a last minute change of plan." He leaned the chair back as it lit up and concentrated on checking the power levels. The connection to the city slid into place effortlessly and he smiled at her energetic welcome that sent tingles down his spine.

"What's our status?" asked Rodney as he connected his laptop.

"We have enough power now," the colonel responded. Eyes closed, he frowned. "We have some Asurans that aren't covered. I'm sending you the coordinates. See if Ronon has someone to cover them. We have to take them all out at once, especially now that we've hit one."

Rodney touched his radio. "Ronon, we have two Asurans at Level Four, Sector C, near the transporter. Do you have someone?"

"Teyla can get them."

"Good. Let us know when she'd in position." Rodney looked back up at Sheppard. "Give her a second to get in position. What about the chair?"

"She's ready. Everything's ready to power up. We've got to hurry though, they're coordinating a search for us. Atlantis wants them out of here." John frowned, anger crossing his face. "They're hurting her."

Rodney opened his mouth to question the statement, but suddenly touched his radio and listened. "They're ready."

"Go!" said John. As he heard Rodney conveying the message over the radio, he began firing drones, focusing his anger on the destruction of the Asuran ship now orbiting the planet. He fired wave after wave until the ship began breaking apart and finally disintegrated into nothing but space debris. Atlantis showed him the victory, sharing the thrill of watching the destruction with her favorite son.

Reports began flowing in through his connection. Atlantis told him of the destruction of Replicators all over the city and he smiled when he realized they were going to succeed.

"The ship is destroyed!" yelled Rodney. "We're doing it. Asurans are falling all over the city." The team from Earth listened as radio reports began coming in.

"We won? We actually won?" asked Woolsey nervously. His face was pale and his hands were shaking, a testament to just how afraid he had been. He looked down at the floor and put one hand on the wall for support. "I just knew we were going to die," he said softly.

"Well done," said Helia, her expression mirroring her surprise at the victory. "I may have miscalculated the value of your presence," she said thoughtfully.

Rodney grinned and nodded. "Well, it's a common mistake. Some of us are actually quite smart. I'd be happy to share some of the many things we have learned and the advancements we've made since coming here."

"Rodney, I think we can worry about that later," said Elizabeth, but she was smiling as well.

"They're gone, all of them," said John hoarsely. The chair deactivated and returned to its original position. "She's safe now."

Helia walked over to stand beside the chair. "Colonel Sheppard, I think you and I have much to talk about. I have never known anyone to connect to the city on that level, although I have heard stories about a very few individuals in the past. There may truly be a place here for you if you are interested."

John grinned broadly. "Oh, I'm interested all right. I've really missed her." He pushed himself out of the chair and took a step toward the door. "I think we should go hook up with . . . " He stopped and put one hand to his head, a sharp pain moving like lightning from the base of his skull to his temples. He could feel his legs giving way, but couldn't seem to call out a warning or ask for help. As he fell forward, voices gave way to garbled noise and darkness, leaving him unaware of the hands that caught him and lowered him to the floor.

TBC