Lost to the Phantoms

Disclaimer: I do not own Stargate: Atlantis or the characters, which is probably a good thing.

Note: This is an AU of season three's Phantoms. Actually I wanted to make this a part of a longer fic, but I don't have the time. Maybe someday.

Also, considering the episode there are deaths.

"Colonel Sheppard, this is base, please respond." Elizabeth must have heard Dr. Zelenka repeat this a hundred times since they first realized something was wrong on the planet. Her heart beat fast as Ronan's voice came over the radio, the first response from the teams off-world in hours.

"We need the Deadalus. The DHD's dead."

Elizabeth found her voice. "Deadalus will be there in about five hours. Ronan, what happened? Where's Major Sheppard?" and Rodney "We've been trying to make contact and no one responded."

The pause sat in the pit of her stomach. Something was wrong. "We need medical supplies and body bags. A lot of body bags."

Her mouth felt like cotton. "How many?"

"We lost seven. Only need six bags. Two are wounded, but Beckett says they'll be fine."

"Who…"

Ronan interrupted her. "Gotta go, Beckett needs me to deal with Sheppard."

The radio connection fell to static, leaving Elizabeth to exchange shocked and worried looks with Zelenka. The scientist was the first to quietly vocalize the thoughts of everyone in the control room. "Who do you think…?" He trailed off, not willing to think about it.

Elizabeth could not help but think about it. Seven dead. There were four on Leonard's team. Four on Sheppard's team, plus Beckett and the four extra marines she sent with them. That meant there were only five survivors. Three were Beckett, Sheppard, and Ronan. She hated herself for hoping that one of the other survivors was Rodney, because that meant she was wishing someone else dead. But Rodney was her friend, more so than others in Atlantis. She was not sure when it happened, but the thought of the snarky scientist seriously wounded or dead made her shudder.

Shaking her head, she mustered up her leader face and ordered that medical supplies and body bags be sent through the gate. She knew she could not risk sending any more personnel without knowing what was on the other side, but it was all she could do not to put on a combat vest and go herself.

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Elizabeth paced back and forth in her office, waiting for news, any news. Zelenka continued to try and make contact again with the off-world team, but to no success. She had resigned herself to the fact that she would have to wait for the Deadalus to return with the survivors and the dead. Her father's pocket watch lay on her desk, mocking her with its constant ticking, telling her that all she could do was wait and do nothing but stand and look leaderly.

A voice came over her radio, "Dr. Weir, the Deadalus just exited hyperspace. They said they're beaming everyone to the infirmary."

Her voice caught and she had to cough before she answered. "Thank you, I'm on my way down."

She never got a chance to even open her door. A bright flash blinded her for a moment, before she blinked her eyes and saw Colonel Caldwell standing next to her. "Hello, Dr. Weir."

Nononononono cried her heart as she saw the saddened look on the old soldier's face. Forcing herself to speak calmly, she asked, "Colonel, I need to get down to the infirmary to see my people."

"I need to talk to you first, tell you what happened."Part of her wanted to scream and run from the room, but she anchored her feet and looked him defiantly in the eyes. When Elizabeth did not say anything, Caldwell continued. "We found them on the planet, made radio contact with Dr. Beckett. He confirmed seven dead, four in need of medical attention."

Weir interrupted. "When we made contact, Ronan only mentioned two wounded."

Caldwell gave a faint smile that did not reach his eyes. "He wouldn't mention his own wound, though it was superficial. No, Ronan had a gunshot wound to the arm; Teyla was shot in the leg. Keagen was the most badly injured, shot in the stomach, though the doctors say he'll be fine."

"And the fourth?"

This was when Caldwell hesitated, his eyes grim. "Colonel Sheppard had a nervous breakdown and Dr. Beckett had to sedate him."

Nervous breakdown? Elizabeth felt a cold chill run down her spine. Anything that caused the stalwart soldier to breakdown had to be awful. "What happened?"

Caldwell took a deep breath, his gaze never quite meeting Elizabeth's. "Apparently a generator on the planet caused people to hallucinate and attack each other. Leonard killed his men, then blew up the DHD because he thought Sheppard and his team were Kull soldiers. He also shot Teyla who was unaffected by the generator due to her Wraith DNA. Ronan started hallucinating Wraith, while Sheppard thought he was back in Afghanistan trying to save his friend. Dr. Beckett wouldn't talk about his own hallucinations, but I have the feeling they were pretty awful. They were only saved from killing each other when Teyla tricked Sheppard into pulling the plug on the generator."

Elizabeth frowned. He had not actually answered her question, though what he had said was frankly heartbreaking. "Colonel, I meant what happened to Sheppard that made him suffer from a nervous breakdown?

Caldwell was definitely trying not to look at her. "He…shot Dr. McKay, apparently thinking he was a Taliban fighter."

The coldness settled into her stomach as she sucked in a breath. "And?"

The colonel forced himself to look Elizabeth straight in the eyes. "And he had a breakdown when he realized that he had killed his teammate."

Elizabeth thought her heart had stopped, almost hoped it would. She felt her knees give out and only by Caldwell's quick thinking and help was she able to collapse into a chair instead of onto the floor. "Rodney?"

The colonel, whom she had once thought of as cold and uncaring, knelt in front of her and grasped her hands, his face full of compassion. "I'm sorry Elizabeth. There was nothing anyone could do. Even with a full surgical team and all the supplies in the galaxy, Dr. Beckett wouldn't have been able to save him. I'm sorry."

That finally broke Elizabeth. Despite her best efforts, she began sobbing in her chair, Caldwell's hands on hers, a poor substitute for the strong, lively hands of her best friend who was even now being transported to the cold sterility of the Atlantis morgue.

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The strength of Atlantis fell apart after that. Colonel Sheppard never really recovered from killing his friend and soon requested a transfer back to Earth. The last Elizabeth heard, he had quit the Air Force and was working on his PhD in astrophysics while flying a crop-duster in his spare time.

With her own grief, Teyla soon left to live on the mainland with her people. She was in regular contact with Atlantis, but the communication was always cold and aloof. Elizabeth did not blame her; it was Teyla's way of separating herself from the loss of her Atlantis family.

Ronan stayed, surprisingly. She figured he felt an obligation to protect that which Rodney loved, Atlantis and her people. The tall Satedan was often seen patrolling the hallways, always pausing by the empty lab of his snarky friend who would never return. Most of all, Ronan was Carson Beckett's shadow, protecting the doctor from all dangers, including his own grief.

Carson became colder after Rodney's death. The doctor had learned his lesson on making friends in that dangerous city. He kept a distance from everyone, pretending not to hear the whispers that followed him. "That's the guy who helped the Hoffan's kill half their population. He turned a Wraith into a human who ended up killing men and endangering Atlantis. And he left his best friend to the mercy of a hallucinating colonel when he followed a dead guy into a forest."

As for Elizabeth herself, she too pushed people away. She was the efficient leader who everyone obeyed and no one knew. By day she calmly sent more people to their deaths, and by night she wept into her pillow as the face of Rodney McKay haunted her thoughts. She would cry until she had no more tears and then fell asleep, awaiting the next day where she would live alone.

And Atlantis continued on.