Disclaimer: I don't own Supergirl or the characters. This is written purely for fun.
A/N: This is set after the end of Season 3. I have made some assumptions about what happens, so at the start of this story the following is true:
1. Lena knows who Kara is (and Kara knows she knows), but they have had a huge fight and Lena looks like she has turned/is turning to the dark side.
2. Mon-El has gone far far away. You can chose if that is to the future or somewhere else - he won't be part of this story.
3. Sam is not dead, but is not part of this story.
4. Ruby is not living with Alex.
Synopsis: Set after the end of season 3, as Kara and Alex try to overcome everything that happens to them, they find themselves in the middle of new dangers. Dangers which causes everyone to question their allegiances.
"You okay?" Alex asked as she sat next to Kara on the couch.
"No." Kara said pulling her knees up to her chest.
"Come here." Alex said pulling Kara into a hug.
"Sorry." Kara apologised.
"For what?"
"The last few weeks have not exactly been easy on you either."
"Worse on you." Alex said.
"I'm not so sure." Kara said. "I think it was worse for you. I just wish I could be as strong as you."
"You are strong. You're Supergirl." Alex said. "Without trying to sound like you, don't give up on Lena, especially if you buy the Back to the Future theory of time travel."
"You got me a DeLorean so I can go back and fix everything?" Kara asked pulling away from Alex.
"No." Alex smiled. "I meant in that film when Marty changed history it was immediately obvious in the past as the photo changed."
"Not following." Kara said.
"Mon-El was only able to be on Earth because L-Corp created a cure in the future. If Lena really has turned why would any future version of L-Corp help aliens and if L-Corp didn't create a cure Mon-El would have started getting ill...actually he would have died."
"The cure is four hundred years away, anything can happen. Someone else could buy up L-Corp." Kara argued.
"Or L-Corp continues on the same path as Lena tried to set it up on." Alex said.
"Even if that is true, she lied about having Kryptonite. She lied about having the ability to make it."
"And we lied to her about working for an organisation that was trying to hunt her mother. An organisation that kept Kryptonite and used it on you." Alex argued.
"Do you trust Lena?" Kara asked.
"No." Alex confessed. "But I never really did. But Lena was your friend, you trusted her when no one else did."
"Why do all my friends lie to me?" Kara asked. "Lena about Kryptonite, James about Guardian, Winn about Siobhan."
"It's a human thing." Alex said. "But if I believed any of them had lied to hurt you I would have taken them out."
"Thank you." Kara said smiling slightly. "Do you think J'onn can handle things for a few days?"
"Sure. Why?"
"I need some time away from here. I was thinking of going to my cousin's fortress."
"Want me to come?"
"I need some time alone." Kara said. "I'll be back for work on Monday, I promise."
"You sure?" Alex asked.
"I am."
"Do what you need to do, I handle J'onn." Alex said.
-00-
"A break could do her good." J'onn said the following day as Alex explained about Kara.
"I hope so." Alex said.
"A break could do you good as well." J'onn pointed out.
"We could all use a break." Alex said. "But Kara said she wanted time alone."
"I meant you could take a few days for yourself." J'onn offered.
"I'd get bored." Alex shrugged. "Besides someone has to train the new recruits."
"Don't push them too hard. At least in their first week." J'onn said as Winn burst into the room.
"Hey guys. I don't know if it is anything but there was a report this morning of some weirdness at the old psych hospital on the East side."
"Define weirdness." J'onn said.
"Sounded like something out of poltergeist."
"Probably kids messing around." Alex said.
"But it could be something else." Winn pressed.
"When did you start believing in ghosts?" Alex asked suspiciously.
"I don't." Winn said. "Okay fine...always. But this is the first time I have had access to the tools I need to investigate."
"Stay here. I'll take him." J'onn said to Alex.
"Really?" Winn asked happily as Alex mirrored his word, but the tome full of doubt.
"Really. Besides you need to train the new recruits." J'onn said.
-00-
"Again." Alex ordered waiting for the recruit to pick themselves off the floor. "This time don't make it so obvious."
"Just need a minute." The recruit said still on their knees.
"You going to say that to the aliens trying to invade this planet?" Alex asked.
"No." He said as Alex heard some muttering from the other recruits.
"Problem Clarke?" She asked staring at one of the other recruits.
"No ma'am." He replied.
"Sounded like a problem. It sounded like you were saying Supergirl would buy you the time you needed to recover."
"You heard that?" He asked sensing trouble.
"Always pay attention to your surroundings." Alex said looking round the group before saying. "Yes Supergirl can buy us time, but she is not our shield. Officially she doesn't work for this organisation. Out there, in battle, you depend on yourself and you depend on your team. Sometimes Supergirl won't be part of that team so get used to fighting like you mean it." She went on as the door opened.
"Sorry to interrupt ma'am." Vasquez said. "But you are needed in the med bay now."
"Keep sparring." Alex ordered as she followed Vasquez out of the room. "What's wrong?" She asked.
"It's the Director." Vasquez said. "He was hit by some sort of weapon."
"How bad is he?"
"I don't know. He is being brought in now. All I know is he's unconscious." Vasquez explained.
"And Winn?"
"He's fine as far as I could tell."
"Get a team ready, I want that hospital secured." Alex ordered.
"Yes ma'am." Vasquez said returning to the control room moments before J'onn was wheeled through the DEO on a gurney. When he arrived in the infirmary Alex immediately started running tests. As she did so she looked at one of the Agents who had brought J'onn in and asked.
"What do you know?"
"Not much. There was some sort of energy weapon that fired at the Director moments before it exploded. As soon as he was hit he went down and has been out of it since then. Winn is still at the hospital trying to collect evidence."
"I can't see any wound." Alex said "Where was he hit?"
"On the torso. But the energy didn't seem to hurt him. I mean it did as he went down, but there was no wound and no damage to his uniform."
Frowning Alex started a more thorough examination.
-00-
"How is he?" Winn asked as he entered the infirmary three hours later.
"He seems to be in a coma. Physically there appears nothing wrong with him, but he won't wake." Alex said. "Did you manage to salvage the weapon?"
"I have every piece that was left….whether it is enough to figure it out I don't know, but I'm getting right on it."
"Before you do, what exactly happened?"
"We went to the room where all the activity had been reported. Billings entered first and everything seemed fine. I went in and started running scans. There was nothing out of the normal. Then all of a sudden there is a spike in my readings and J'onn is blasted."
"When did J'onn enter the room?" Alex said.
"I don't know exactly." Winn confessed.
"Could it have been his presence that triggered the weapon?"
"Maybe. I can go through the logs in more detail." Winn said. "And it would explain this." He added handing Alex his tablet which displayed a Martian symbol. "It was in the room."
"Looks like they wanted J'onn to go there." Alex said. "Concentrate on the weapon, I'll do what I can here." She continued before adding. "This isn't your fault."
"He only went there because of me." Winn said.
"As soon as he had heard about the symbol he would have gone anyway." Alex said. "Right now we have to figure out what happened and how to fix it. We can worry about stopping something like this happening again later."
"Okay." He nodded before asking. "Do you want me to try and figure out a way to contact Kara?"
"No. She needs a break and currently there isn't much she can do." Alex replied.
-TBC...
A/N: Thanks for reading and reviewing