Excerpts from Richard Woolsey's personal report to Stargate Command:

It is in my opinion that Stargate Command has made the best decision in closing the wormhole between Atlantis and Earth. This new alien threat is still mysterious enough and powerful enough for us to not know whether or not we have the strength to effectively resist another attempted takeover of the city, not to mention the extreme power drain the Stargates experience every time we dial between the Pegasus and Milky Way Galaxies. Atlantis will need all its resources to work on a solution in the meantime …

As to your query on Lieutenant Colonel John Sheppard's competency to command, Dr. Keller informs me that he is of sound mind and body. His ordeal while a captive of the Ancient, Janus, was a long and complicated one. It appears that Colonel Sheppard's ancestors were directly related to the Ancient General Icarus …

While we have no record of Icarus in our archives, we have learned — through our interactions with Colonel Sheppard while under the influence of the drug, and Janus himself — that Icarus was a feared warrior and commander of an Ancient ship called the Labyrinth. He fought many enemies of the Ancients, including the Goa'uld in the Milky Way and the Wraith in Pegasus, and was responsible for completely eliminating the fleet of At'um, the predecessor of Ra. This feat in itself is worth mentioning as Ra himself was unable to overthrow At'um …

The problem with Icarus and the Council based on Atlantis thousands of years ago seems to have emerged after a mission he was obliged to carry out while General Icarus was stationed on Earth. It seems that he was sent to Earth alone to exploit an enemy of the Ancients — serving undercover, perhaps — but once he had eliminated the threat, the Council forced him to leave Earth … We suspect it was somehow due to our own Icarus legend emerging and that the Ancients did not want him to be worshipped as a god if he returned alive — unlike the Goa'uld. Icarus was upset about this for years afterwards as he had built a life for himself there … It seems that Janus also tried to manipulate him into planning a coup d'état of the Council.

According to Colonel Sheppard, Icarus was not interested in overthrowing the Council — only Janus wanted this. Icarus wanted only to pursue his duties, which included destroying any enemies of the Ancients. Janus wanted to pursue his own agenda, which included illegal experiments and resulted in him being banished to a far world in the Pegasus Galaxy without access to a DHD. This planet is where we believe Colonel Sheppard ended up being held captive and experimented on himself, alongside an army of alien beings or genetically enhanced beings that Janus had created in his own personal war on the Wraith. (Our conclusive genetic analysis on these soldiers is awaiting Dr. Jennifer Keller's full report.)

We believe that Janus died on this world and created the hologram to continue his work without him. He must have also created his own DHD device which freed the soldiers he had created to leave the planet … According to Colonel Sheppard, he was sent on several missions to destroy the Wraith while under the influence of the drug. (Please read Dr. Keller's enclosed report on the drug properties and device which was implanted on Colonel Sheppard.) …

Although these missions appear noble and further our own cause, Colonel Sheppard advised me that Janus and his soldiers will stop at nothing to destroy the Wraith. If this means that civilians or innocents stand in the way, they will also be eliminated. Janus' soldiers are single-minded when it comes to destroying the Wraith. It is due to this that we cannot ally ourselves with them. If we don't become one of them then we will also be eliminated …

Colonel Sheppard believes that Janus wanted to retake Atlantis and weaponize it in order to pursue the Wraith across the Pegasus galaxy … In their initial attack, we lost three men, however, I believe we could have lost far more if Colonel Sheppard were completely under Janus' control …

Regarding your query as to whether or not we can attempt to negotiate with the Janus AI program and bring him to our side in the fight against the Wraith, I have been strictly advised by Colonel Sheppard not to do so. His reasoning is that the hologram is a near perfect replica of the original Janus himself. If this is so, as I stated before, the original Janus would stop at nothing to eliminate the Wraith. He would put all of Atlantis under his control, including turning our people into super-beings against their will. We have already seen this demonstrated with the drug and device that we had to surgically remove with great difficulty from Colonel Sheppard … Although it appears we all want the same thing — the elimination of the threat of the Wraith — the cost would be too great to justify …

I tend to agree with Colonel Sheppard along these lines. I have seen firsthand what these aliens can do. They are powerful and not afraid to kill anyone who stands in their way. Their end goal is the destruction of the Wraith, and if we stand in the way of this goal we will also be destroyed …

I will send this message with the Odyssey when she arrives in the coming weeks. It's a shame the Daedalus was destroyed by the Replicators but I'm sure we will manage our own airspace with the puddlejumpers and F-302s that we have here. Perhaps we will have managed to solve this problem in that time, or perhaps not. Regardless, it has been an honor to serve under the SGC and I hope that we will be able to restore regular channels one day.

Richard P. Woolsey

Commander of the Atlantis Expedition

The day Sheppard was released from the observation room and moved to the infirmary he was able to walk on his own, but was escorted at all times by at least four Marines. He was weak after his ordeal with the drug, but his mind was clearing and he was able to hold a conversation for more than five minutes before feeling exhausted again. Keller insisted that he stay in the infirmary until they administered the last dose of the drug so that they could monitor his progress. Woolsey insisted he remain under guard until they were sure he was completely in his right mind again.

Sheppard had to have several sessions with Heitmeyer as part of the decision on whether to declare him fit for duty or not, but she told Woolsey there was a definite darkness hanging over the Colonel's head. Guilt over his capture and subsequent betrayal of Atlantis, plus the deaths of the men in the 'gate room had made him reluctant to want to return to duty. Thankfully, he no longer seemed to be confused as to whether he was Icarus or Sheppard, which was the major issue that she was most concerned about.

Woolsey wasn't sure they could afford to have the Colonel discharged permanently. If there was an impending war with a vengeful Ancient hologram who had a seemingly all-powerful army at his disposal, Woolsey knew that Sheppard was their best hope for survival. In the past he had protected Atlantis from the Genii invasion and the Wraith and had put his own life on the line multiple times for his people. Although Lorne was good, he was no Colonel Sheppard.

Sheppard was utterly fearless, trained to put his life before others and completely willing to do so at all costs. If it weren't for the black mark on his record back on Earth, Woolsey was sure that Sheppard would have been promoted by now. But the reckless flyboy in the man made sure that he stayed under the radar. Only those close to him knew his true colors and where his loyalties lay.

But that man seemed to be a distant memory now.

When Woolsey walked into the infirmary, he saw Sheppard sitting up on the infirmary bed with his eyes closed. He was dressed in black scrubs that made his pale skin stand out all the more against the dark fabric. Despite the long days of withdrawal, he looked surprisingly well. But as he heard Woolsey approach and opened his eyes, Woolsey read the utter exhaustion in his face.

"How are you doing, Colonel?" Woolsey asked, pulling up a chair.

Sheppard shrugged. "Doc says I can leave tomorrow. Been clean for five days now. Just have to report back every day for a bit."

"Dr. Heitmeyer has also tentatively cleared you for duty," Woolsey said, "so I've lifted your guard detail. But she says that you are not sure you want to come back."

Sheppard leaned his head back on the pillow. "I was compromised," he answered slowly. "It wasn't like the Wraith queens. They can make you do things, but your mind is still yours. This … This was different. Janus changed how I thought. He changed who I believed I was. I really believed those aliens were my brothers and that Atlantis was the enemy. I really believed I was Icarus. I … I'm afraid he might do it again. If not to me then to someone else."

"Janus can't touch you now," Woolsey said. "The iris appears to be working. He's tried dialing in multiple times since your return and they have been unable to get through. Dr. McKay is also working on a way to block their access so we are able to dial out at will and resume normal operations."

Sheppard closed his eyes. "But we can't keep the 'gate closed forever and we might run into them out there."

"Running into the enemy anywhere has never stopped you before, Colonel Sheppard," Woolsey snapped.

Sheppard opened his eyes, surprised at Woolsey's tone.

"You have gone out multiple times on missions, never afraid of encountering the Wraith or Genii, even when they have done unspeakable things to you and your team. You have persisted in making this galaxy a better place and fighting back against the enemy. These aliens are no different. They may be powerful, but you need to have faith that the people of Atlantis will find a way to fight them — like we always do. We will find a way to either negotiate or push back. But we can't do it without you."

"You don't understand how Janus works," Sheppard pressed. "He isn't just after the Wraith. He designed these soldiers to eliminate anything he sees as a threat. He sees Atlantis as a threat because of what they did to him and Icarus. It doesn't matter if we're on the same page. Yes — we both want the Wraith gone, but he will literally stop at nothing to get what he wants. And he wants Atlantis and her weapons. He will kill anyone in his way — Wraith and human alike."

"I can be a fair negotiator if need be," Woolsey countered.

"I have no doubt," Sheppard responded. "But Janus is not a living, breathing Ancient anymore. He's something else. A twisted AI who believes that I'm his nephew. And the technology he's developed is unlike anything I've seen. He disintegrated entire Wraith motherships in minutes. He could do the same thing to Atlantis if we provoke him enough."

"We won't let him," Woolsey said firmly. "Atlantis has stood up against many enemies in the past. We are prepared to do so again — with your help."

Sheppard shook his head. "Just ask Stargate Command to send someone else. I'm not sure I'm fit for duty. There are plenty of people back on Earth who would jump at the chance to command Atlantis against a new enemy."

"We are cut off, Colonel."

Sheppard sat up, suddenly alert. "Cut off?"

"Stargate Command has closed the wormhole between Atlantis and Earth in light of this new threat. We have only ourselves, and we need you."

"Lorne would do a fine job —"

"No. He has refused command. He has taken over your duties for now but has explicitly said that once you are declared fit for duty he will resume his normal duties so you can resume yours."

Sheppard shook his head, muttering under his breath.

"Frankly put," Woolsey continued, "I understand that you have been through a lot. In normal circumstances we would not be in this place right now. You would probably be relieved of your command and possibly court martial-ed. But we are not in a normal situation anymore — nor may I argue may we ever be in a normal situation. Atlantis is alone and we have a new enemy — an enemy that you understand intimately. You need to step back up to the plate. Major Lorne is a fine leader, but he is no Lieutenant Colonel John Sheppard. We need you."

Sheppard looked at Woolsey for a long moment, then said softly, "Fine. I'll resume my normal duties. But once we figure out what to do about these aliens and are able to reestablish a connection with Earth, I respectfully request to be relieved of duty."

Woolsey also paused before answering. He knew that Sheppard desperately wanted to resume command, but he also knew that Heitmeyer had said that he would do anything he could to protect his people. In this case, Sheppard felt the best way to protect Atlantis was by removing himself from command.

"I accept your conditions," he finally said. "On the terms that we are also able to find someone I deem a fit replacement."

Sheppard wordlessly offered his hand and Woolsey shook it, knowing that he would do anything he could to keep Sheppard in command of Atlantis.

"I expect to see you bright and early on Monday morning," Woolsey said with a smile, standing.

Sheppard gave him a sloppy salute. "I'll be there."

And Woolsey hoped the glint he saw in the Colonel's eyes was a hint of the fighter that he knew the man could be.