A/N: Thanks for the comments.

Guest - Lex is not the mastermind in this.

Alexfan - Alex will be defending her sister. Lex will be working with Lilian so knows everything she knows.

"Madam President?" Supergirl asked as she opened her eyes and saw the former President look down at her from an adjacent cell.

"That title seems a little pretentious, especially in here."

"Where are we?" Supergirl asked looking round trying to ignore her nausea.

"The latest incarnation of Cadmus. Much like the first version it is supported by the government and they will do everything they can to kill aliens. What I haven't figured out is how you ended up here."

"President Baker poisoned me and handed me to Lex Luthor."

"That is a big risk for him to take. Your absence will be noticed." Marsden mused.

"He said he needed me out of the way." Kara said as she tried to move.

"Careful. You have been very sick." Marsden warned.

"How long have I been in here?"

"A coupe of days."

"A couple of days?" Supergirl asked surprised as she forced herself into a seated position.

"Being semi conscious and sick for two days might be the preferred option." Marsden warned.

"What have they done to you?" Supergirl asked.

"Lots of tests, but something tells me I'm still needed so the worse is some way off. Not everyone is so lucky. Some have been taken from their cells and not come back. Some have come back traumatised." She said nodding to another cell.

"Is that Jensen?" Kara asked, recognising the man sitting in the cell hugging his knees. "So that photo was real. He is alive."

"Something I am not sure he is happy about." Marsden said as they heard footsteps approach.

"Oh good, you are awake." Lex greeted as he stood outside Supergirl's cell.

"You won't get away with this?"

"Technically there is nothing to get away with. I have my orders, from the President himself and in writing. But fortunately for you I plan to follow those orders. You see I need to come up with ways of killing Kryptonians. But I only have one to test on. And I can't risk losing that test subject, so for now death will not save you."

-00-

"Director Danvers we have a problem." Vasquez said.

"What?" Alex asked turning and looking at the screens where someone who looked just like her sister was destroying a power plant.

"What the hell is Supergirl doing?" Haley asked.

"That is not Supergirl." Alex said. "People are getting hurt. She wouldn't do that."

"Why not? She did before, when she was under the influence of the other Kryptonite." Haley pointed out.

"She didn't hurt anyone then."

"She threw Cat Grant off a roof."

"And then caught her."

"She broke your arm." Haley argued. "But debate is pointless. Supergirl or not. We need to stop her. Team Alpha and Bravo get out there." She ordered before noticing Alex was typing at a console. "What are you doing?"

"If you are right and that is our Supergirl and she has been exposed to something we need to figure out what so we can reverse it." Alex said. "I am pulling up spectral imagery from her last know whereabouts."

"What if she was captured and given something?" Vasquez asked.

"Even more reason to figure out where she went." Alex replied.

"Ma'am." Agent Reese called out. "Supergirl has left the area."

"Where did she go?" Haley asked.

"I don't know, she flew off too low and fast for radar to track her."

"Find her. That is the priority." Haley ordered. "Agent Dox, finalise the anti-Kryptonian weapon. I expect it completed by tomorrow." With that she walked out of the command room. As she left Alex once again pulled out her phone and tried ringing Kara, sighing when it once again went straight to voicemail.

"Director Danvers can I talk to you?" Brainy asked.

"Sure." Alex said leading him to one side. "What's wrong?"

"Firstly there is an alert set up that will notify us the second Kara's phone is switched on. Endlessly ringing her is pointless."

"Anything else?" Alex asked.

"Nia dreamed this as well."

"Dreamed what?"

"The destruction of the power plant, at Supergirl's hand."

"Why didn't you mention this before?"

"We were more focused on Supergirl's detention." Brainy said. "Although in hindsight that may have been a mistake."

"What else did Nia dream?"

"Nothing, as far as I know."

"Work with J'onn and Nia. Try to extract any information from those dreams that you can."

"And the weapon?"

"Make sure it is not lethal and won't do any permanent damage."

-00-

"Ma'am." Vasquez said knocking on the door a few hours later.

"What is it?" Alex asked.

"The Children of Liberty are back." Vasquez said before turning on one of the screens and navigating to a webpage. "This went live a few minutes ago."

"Inhabitants of Earth, I am Agent Liberty and I am here to free us from the shackles that aliens have put on us. You have all seen the video. You have all seen how the self proclaimed alien saviour of Earth has turned on us, just like we warned you. If Supergirl can't be trusted no alien can. We must move to protect ourselves and free ourselves before it is too late. To any aliens out there you have forty eight hours to leave this planet peacefully. After that you will be detained until transport can be arranged. To all humans we have set up hotlines and message boards. Please report all alien activity there and the Children of Liberty will clean up our city, then our country, then our planet."

"Start monitoring those message boards and hotlines. We need to protect the-" Alex started only to be cut off by the Colonel.

"Director Danvers, it is the role of this organisation to protect the Earth from alien threats. This does not fall into that remit. Stopping Supergirl does." Haley warned. "Focus on your job, which has nothing to do with the Children of Liberty."

-TBC...

A/N: Thanks for reading and reviewing.