Imagine that Lockwood got caught and arrested later than in 4x08 and the rest with Manchester Black and the Elite will end rather quickly than how it was dragged out and Lex didn't happen and the president of the U.S. isn't Baker, who was in Lex's pocket but Plastino, the president of the U.S. of Earth Prime after the Crisis, since don't get me started on how stupid and lame villain Lockwood was and while I enjoyed the Lex and Red Daughter arc, it just doesn't work for this story.

Disclaimer: I do not own DC Comics or the CW TV shows Arrow, The Flash, Legends of Tomorrow, Supergirl or any other characters or elements pertaining to the mentioned franchises.

"Alex! Brainy!" Kara called out as she approached one of the agents. "Hey, Hartmann, have you seen agent Dox and Alex?"

"They were in the labs in the middle level, last I saw them." Hartmann said.

They went downstairs and saw Alex dead on the ground with Nia curled to ball in the corner, sobbing as Kara felt her heart shatter. "No…" Kara knelt towards Alex, trying to wake her up, shaking her. "Alex? Alex?" After a few moments, she broke down in tears, sobbing into Alex's chest.

"Nia?" J'onn turned to her as she still stared in shock. "What happened?"

"I couldn't leave her like this…" Nia whispered.

J'onn knelt towards her, hugging her as she sobbed.

Barry, Cisco, Caitlin, Ralph and Sherloque came from Earth-1 to talk as they were all in the conference room. "Brainy did this?" Barry asked. "Did he…"

"He killed Alex." Kara said lowly.

"He didn't kill Alex!" Nia exploded as she got up. "That wasn't Brainy! It was his goddamned ancestors who did it! They… somehow he got rebooted because of that virus and they took over his body! Brainy would never have hurt her!"

"Nia…" J'onn tried to console her but she ran off, clearly still in shock.

"Brainy would never hurt Alex, not out of his own volition." Kara said.

"We know, Kara." Cisco assured.

"What virus?" Barry asked, confused.

"What exactly happened?" Caitlin asked.

Kara wiped her face, trying to keep her tears at bay. "It was few weeks after Mar Novu."

Colonel Haley cleared her throat. "Supergirl, with all due respect, I advise against divulging DEO's and governmental secrets to strangers…"

"They're not DEO but they're our allies, Colonel. We trust them." J'onn said and Colonel Haley sighed.

"Very well. If you vouch for them, I'm willing to trust them. For now. But anything happens, I'm holding you responsible." Colonel Haley said as she left.

"Your new boss?" Barry asked.

"Yup." Kara muttered. "Be careful around Haley, she's a hard-ass and by-the-book."

"Got it." Cisco nodded. "So, what happened?"

Three months ago

"Are you sure it's here?" Supergirl called out as she was flying in the air, using the special suit from Lena.

"The coordinates are a match." Brainy said, flying next to her with his Legion ring.

"Be careful. We don't know what are we dealing with." Alex called out from DEO.

"Don't worry, Director Danvers, we will be careful." Brainy assured as they neared the ship. "It's ancient. Coluan…"

"Like your ancestors?" Kara asked.

"Yes." Brainy said. "It's fascinating…"

Suddenly, an alert bleeped. "Oh, no." Alex panicked.

"What is it?" Kara called out.

"Uh, someone fired a missile from the ground." Alex said.

"Lockwood and the Children of Liberty." Kara realized. "Can you intercept it?"

"I can't make it in time." Alex said. "And you can't stop it, it's irradiated with red sun."

"No but I can slow it down." Kara said as she dove towards the missile, trying to slow it down.

"I'm downloading the data." Brainy said as he plugged into the ship's computer and quickly downloaded the data into his brain.

"Brainy! I can't hold it for much longer!" Kara cried out.

"Got it!" Brainy said as he flew away from the ship, while Kara let go of the missile as it blew the ship up.

"Liberty! Liberty! Liberty!" Children of Liberty cheered before DEO agents surrounded them, with Alex in charge.

"Benjamin Lockwood, you are under arrest for acts of terrorism and threatening U.S. civilians!" Alex yelled.

DEO

"Mr. President." Alex greeted the U.S. president Plastino.

"Director Danvers." The president shook his hand with her. "Thank you for apprehending this terrorist called Agent Liberty."

"His followers are in disarray but we're working on hunting them down." Alex assured.

"Good to know. Anything else I should know about?" The president asked.

"We're working on protecting both alien and human citizens here, I can assure you." Alex said.

"This radical movement Mr. Lockwood led, has been quite provoking." The president shivered. "And then there is still this Manchester Black…"

"We're working on finding him. Hopefully we can stop him before he causes more trouble." Alex said.

"I'm certain he will try to go after Lockwood, if what you've said, is true." The president said.

Brainy was in the training room, sparring with Nia, who was blindfolded as they exchanged blows.

"Excellent. Your precognitive abilities are progressing." Brainy said before he hit her in the back as she fell down.

Nia put down the blindfolds. "I'm still too slow."

"It's not about speed or strength. It's about instincts." Brainy said.

"I told you, I can't control…"

"Nia. If you don't trust in yourself, you'll never win. There's no room for doubt." Brainy assured her. "Again!"

Nia took a breath as she put on the blindfolds, again sparring with Brainy, landing few hits as she predicted his attacks. "Good!"

Suddenly, he was knocked down as he groaned before he suddenly hit Nia hard as she groaned upon falling down. "Brainy!"

Suddenly, Brainy came to. "Nia! Oh, dear, I'm so sorry." He held her face gently. "I didn't mean to, are you OK?"

"It's just a bruise, I'm fine. I think I need a break." Nia said.

"Yeah, I think that's a good idea." Brainy nodded as she left, while he was starting to shake and have a seizure.

"Collect… collect… collect…"

Suddenly, he came to as he shook his head as Nia neared him. "Brainy. Are you OK?"

"I'm fine, Nia. I'm fine." Brainy said, although it sounded like he was trying to convince himself, rather than her, wondering what was happening to him.

So, what do you guys think?

Please review and let me know if you have enjoyed this and want for me to continue.