The Empire of the Alterra

Authors Note: This story is based on many principles from The Return of the Ancients. But, it will be fundamentally distinct in many ways. Read on to find out.

*I do not own Stargate or any inspirational ideas from Return of the Ancients.

Chapter 1

"What has the IOA done this time," Sheppard asked half-heartedly at Rodney. "Umm, well they plan to destroy Atlantis, take our ZPM and leave the galaxy to the Wraith."

Sheppard knew McKay wasn't joking due to that serious/terrified look on his face. "And how do you know about this Rodney," replied Sheppard. "I um, hacked into Woolsey's computer and discovered the IOA's secret." "Sheppard, if you're with me on this I know how to stop it," Rodney seriously replied. "Follow me."

Rodney led John through a series of twisting corridors until they reached a locked door in an unexplored section of Atlantis. Rodney hooked up his tablet, entered an access code, and the door opened.

Inside was something that looked too much like a DNA altering machine for John's comfort. "Sheppard remember when O'Neill used the Ancient Respiratory of Knowledge," Rodney asked. "Yes, but it almost killed him McKay," Sheppard responded.

"But that was only because his physiology wasn't advanced enough to handle all the information. His body was in a state of flux. Very painful," Rodney lectured. "McKay just get to the point, how is this going to save Atlantis. Woolsey already replaced the marines with IOA corrupted ones. They now have control of Atlantis," Sheppard shot back, feeling a little exasperated.

"I've programmed this machine to transform you and I into Alterra. At that point we wait a few weeks until the transformation is complete. No one will know the difference. Then are minds will be advanced enough to safely handle the Respiratory of Knowledge. The key to saving Atlantis will be in there. I'm sure," Rodney explained.

"That...could work Rodney. Are you 100% sure this is safe. Because if something goes wrong...," Sheppard replied while sitting down into a chair. Rodney looked strait at Sheppard and said, "John, the chance to become Alterra, to literally know the secrets of the universe. Not to mention superpowers. This is a chance of a lifetime. Are you really going to let it go by."

At that point Sheppard looked persuaded. "After all, this isn't the first time I've done something... not sanctioned by my Superiors," John replied. Rodney shook Sheppard's hand and they mutually agreed, "Lets save Atlantis."

Both John and Rodney were ready to alter the course of history by transforming themselves into Alterra. "Now John, this is going to take massive amounts of power from the ZPM, maybe even depleting it. Once we do this, Woolsey is going to have us court-marshaled. We have to get out of Atlantis as soon as we do this." Sheppard nodded in response to Rodney's statement.

McKay also handed Sheppard a Lantean stun pistol and said, "You'll need it." At that point John and Rodney walked into the DNA sequencer and it activated immediately. Within seconds the machine finished and its two occupants fell on the floor, unconscious.

Control Room- Atlantis

Radek was sleeping. He had been up for nearly 40 hours. It was catching up on hime now. Unfortunately, his laptop began to beep rapidly and he woke with a jolt, his glasses almost falling off. He glanced at the screen and really jolted awake when he saw the ZPM levels drop from 70 percent to just above five percent.

He tapped his earwig and said, "Mr. Woolsey you're going to want to get up here now." Mr. Woolsey was not a happy commander. "Why does everyone keep waking me at midnight," he thought. Once he saw the ZPM levels, his mood got even sourer. He turned around toward a tired Radek. "Initiate a city-wide lockdown." "Yes Mr. Woolsey," Radek replied as he punched a few button on the control interface while murmuring in angry Czech.

DNA Sequencer Room- Atlantis

John and Rodney awoke after a few minutes. Sheppard managed to pull himself up to sitting position just to confront a massive headache. "Did it work," he asked. After checking his tablet, Rodney nodded and replied, "We are now both Alterra. It's going to take a few weeks before the full transformation is complete, and we should probably get out of here."

At that point a bunch of guards started to pound on the door. Sheppard and McKay looked and each other and felt a wave of mutual understanding. They both raised their stun pistols and nodded. At that point the door open revealing some un-friendly looking marines. Before they could do anything about John and Rodney nailed them with their pistols and the marines fell unconscious. "Let's get out of here," a weary Sheppard said.

As they rounded a corner they faced another locked door. After checking his tablet Rodney looked at Sheppard and mentally told him to place his hand on door panel and to think about Atlantis. John figured mental communications was another advantage of being an Alterra in progress. When Sheppard did as he was told he found himself in a virtual map of Atlantis and soon found the door he and Rodney were standing at. He just thought open and the door did as it was told. By time they reached the door to the jumper bay all he had to do was think, "open" and the door obeyed. Rodney figured because the Alterra built Atlantis they could override lockouts while the Lanteans couldn't.

McKay and Sheppard ran for the nearest Puddle Jumper and began to dial the Tower. That gave the control room team quite a scare as the gate activated and a jumper descended down from its bay. Woolsey's voice came over the radio. "Colonel Sheppard and Dr. McKay stand down immediately or you IDCs will be locked out. Sheppard payed no attention to him and drove through the gate.

Once they reached the Tower, McKay dialed New Athos and not before long they found themselves parked and cloaked in the middle of a huge forest were Atlantis would never find them.

It wasn't before long that Rodney and John engaged in a mental conversation. "So, what now," John asked. "Well, I've run the calculations and our transformations will be complete in a week," Rodney replied, "John, I wanted to talk to you about the Ancient Head Sucker.

"Okay," John uneasily replied.

"It's more than just their knowledge John, it's their Legacy," Rodney sympathetically said, "A hidden part of the database told me that we need to rebuild their empire. We are the last two Alterra. Now their responsibility is ours."

"Um Rodney that's a lot of responsibility," John said.

"I know, but you have to trust me on this."

"Now let's get some sleep."

One Week Later

John and Rodney took off, headed for the gate. Their genetic alteration was complete, they were now fully Alterra. Rodney dialed a hidden address in the Lantean database, a planet with an Ancient Respiratory of Knowledge. As soon as they rematerialized on the other side of the gate, Sheppard cloaked the jumper immediately as McKay uploaded the coordinates to the HUD. Within minutes they arrived.

John set the jumper down about a quarter mile away from their destination.

"Sheppard are you sure about this, I mean I don't want too pressure you or anything like that," Rodney rambled.

"McKay, look its fine, we have to do what we have to do," John said. At that point they had reached the Respiratory of Knowledge. "Here goes nothing," John said as he stuck his head inside. A few seconds later Sheppard fell to the floor, groaning. Not even bothering to look at his friend Rodney McKay stuck his head into the Ancient Head Sucker and collapsed beside his friend.


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