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Elizabeth walked toward the balcony doors, despite knowing it was stupid. She could hear voices behind her, but she couldn't stop herself from moving toward the windows. The city was rising into the air, the Asuran weapon flooding the shield with light as Atlantis began to escape the planet.
She tapped her earpiece. “John? Are we ready?”
***
In the weeks after the nanite incident, John started going by Elizabeth’s office in the evenings. Well, nights, really. She wasn’t sleeping, even more so than before. He wasn’t the person to try to get her to talk, but he could sit with her as she worked.
His own experience at the hands of the Wraith wasn’t letting him sleep much anyway.
So he sat on the couch and Elizabeth sat behind her desk, or sat in the chair in front of her desk. Always keeping a little distance between them.
Even after they got the city back, Elizabeth was still preoccupied. She was working on translating material from the Ancient databases. She’d started using a legal pad and a pencil, and he’d teased her about going old school, assuming it was some quirk of her study habits. She had smiled a little, and it hadn’t occurred to him that she didn’t want what she was doing on one of the networked computers.
Then one night, she had grabbed the legal pad and sat down on the couch next to him. He didn’t move, shocked by the unexpected warmth of her thigh against his.
Silently, she handed the pad over. For the first time in a long while, he couldn’t read her expression.
He looked down at the legal pad. He read the top page, then read it again.
Three letters were at the top of the page. And below it, a gate address.
***
If Elizabeth was honest with herself, the itch started long before she acknowledged it. Bad decisions being passed from Earth, recalls, questions, Woolsey coming to Atlantis and poking into her decisions and harassing her people. There was a time she was good at this game, but her diplomatic skills had eroded. Or the realities of life in Pegasus had changed her priorities.
Then the nanite infection, which had left her reeling, questioning herself at every turn. Afraid of the questions being asked about her leadership, both in the city and back on Earth.
Then she countermanded orders to save John from Kolya, which only made it worse, even if for her – for all of them – there was no other choice.
If she, John, Rodney, and Carson hadn’t snuck back to the city to stop Hank Landry from trying to destroy the Asurans with a bomb, she wasn’t sure the IOA would’ve let her return at all.
She was allowed to stay and stay in command, fairly sure it was thanks to Jack personally intervening. But the IOA didn’t let up. More questions, inquiries. Requests for reports, including a mandatory evaluation with Kate, who carefully ended the official meeting before letting Elizabeth know the IOA had also asked for an evaluation of John.
That was the moment when Elizabeth saw red. They weren’t just coming after her now. They were coming after her through her people. And she’d be damned if she let them get away with it.
***
Elizabeth only told Chuck that she’d found a new gate address in her translations to get the site added to the list for upcoming missions. John just thought Elizabeth was being overly cautious, but he agreed with her to not discuss what they thought she’d found anywhere they could be overheard until they knew something for sure.
They sent Lorne’s team, with Zelenka, only telling Radek just before the mission what to look for. John wasn’t happy keeping this from Rodney but Elizabeth feared getting his hopes up. And Rodney’s inability to keep his mouth shut.
Lorne’s Ancient gene was strong enough to get the lab door open. There wasn’t much left, but Radek came back with wide eyes and shaking hands.
Once it was confirmed, they had to loop Rodney in. The truth was known only to the four of them. Lorne knew the lab had held research about power sources, but not the whole of it, at least not officially. Atlantis wasn’t a great place for keeping secrets, but nobody said anything on the record. Rodney and Radek worked off Elizabeth’s translations of the schematics, kept on a non-networked computer.
John worried that Elizabeth was being paranoid about all of this, but he went along with it, assuming they would tell the IOA when they had something concrete to report.
Then Ellis arrived, repeating the same mistakes as Landry, the same mistakes everyone on Earth kept making when it came to the Pegasus galaxy, and he realized that, as usual, she’d been right all along.
***
Colonel Ellis was a crystallization of everything wrong with Earth's approach to the Pegasus galaxy. The Asurans weren't the Replicators, and provoking them deliberately was a terrible idea. She knew it with a bone-deep certainty that was difficult to explain to anyone else without calling her loyalty into question.
It was questioned anyway. Ellis grew increasingly belligerent the more she objected, until he made a snide comment about her being compromised by her experience with the nanites and no longer fit for command.
Rodney grabbed John as he tried to jump across the table toward Ellis, but the damage was done.
"This mission has been approved by the IOA," Ellis said, gathering his entourage to depart. He looked from her to John. "I expect your full cooperation. If you refuse, I’m authorized to have you both removed from command until new personnel are sent from Earth."
Ellis walked out, ignoring the explosion of protests behind him, Rodney shouting louder than anyone.
She was aware of how everyone was looking at her. She squared her shoulders and nodding at John and Rodney. She walked calmly out of the conference room, across the control room, and out onto the balcony, where she gripped the railing like a lifeline.
Once the doors were closed and they were alone, she met John’s eyes and saw her own resolve reflected back to her.
John turned to Rodney. "Tell me they're ready."
"Yes! Mostly. They’re complete, it's just, we were going to test the alignment with-" McKay babbled, waving his hands.
"Rodney," she cut him off. "We're out of time."
***
Late one night, when they were both too exhausted to sleep after... actually John didn't remember exactly what crisis that had been, but he and Elizabeth had been sitting in her office and talking. Her translations had been put aside for the moment, and she had asked him what it was like for him to sit in the control chair.
There was a wistfulness in her expression. He forgot, sometimes, that Elizabeth wasn’t connected to Atlantis the same way he was. She was so central to everything in the city, it slipped his mind that the gene therapy hadn’t worked on her and she couldn’t use to the technology like he did.
But then, she was connected to it in a different way.
It was hard for him to explain without sounding crazy, but Elizabeth had been too tired to question it when he said he could almost feel the city thinking.
He felt it now, the city pausing momentarily as he tried to bring the power system online. A flicker of hesitation, almost like the Atlantis was seeking his reassurance. He did his best to project confidence in McKay's work.
One. Two. Three.
The three new zero-point modules McKay and Zelenka had built, based on the information they retrieved from the lab on the planet Elizabeth had discovered in her translations, connected.
There was another beat of adjustment, the power output not precisely the same as the original, Ancient-made ZPMs, but John stabilized everything. He could feel the drain from the Asuran weapon on the shield, and he started the star drive.
The city rose up through ocean and broke the surface of the water. He felt the blast of the Asuran weapon on the shields like an impact to his own body, but the shields held, the new ZPMs holding off the weapon as John aimed for the stars.
As they broke atmosphere, he heard her ask, “John, are we ready?”
"This is Sheppard. We're good to go."
Through his link to the city, he listened as Elizabeth summoned the ships holding Lorne and the other pilots back. When they were safe, she radioed Ellis. “Colonel Ellis, this is Weir. You and the IOA are no longer welcome in Atlantis. Don’t bother trying to follow us.”