The part of Alex that was protector was throwing a massive hissy fit over this idea. The part of her that had spent the last several months watching a sad, lost, and lonely little girl pining for her mother was praying it worked. They had taken Sam out of the holding tank and laid her on the medical bed they'd moved into the room. They would keep her under the red sun lamps as a precaution, even after she woke up. If she woke up. They had no idea what this would do to Sam, what state she would be in afterwards. Alex sighed softly as she stood there watching Lena and Querl as they worked. Then her eyes flicked to the security camera. She knew that Kara was close by, watching the live feed from a safe distance since the room and hallway just outside the door were awash in red sun light.
Alex knew that Kara had her reservations when it came to Querl Dox because he was a Brainiac. She had been willing to work with him in order to take down Lobo and protect Andrew, but trusting him to help in a fight was different than trusting him to separate Sam from Reign.
Using the equations and formulas Lena had created Querl would act like an interface to implement what was explained to them as an antivirus program, or a kind of tech chemo. That was far more intimate than having him blast Lobo with his energy weapons. Alex was starting to wonder if Kara was on standby in case something went down with Reign or if she were waiting to see if something went down with Brainiac 5.
"I appreciate your willingness to accept my offer of assistance, Ms. Luthor." Querl said softly to the dark haired woman beside him. "This means a great deal to me."
There was something in his voice akeen to reverence that Lena couldn't quite understand. Turning to look at him she said, "You make it sound like some kind of honor."
"It is." The young man replied. He looked into her eyes for a moment before explaining, "Though I share Imra's sentiments at having meet Supergirl, I am far more pleased at having met you."
"Me?" Lena replied with genuine surprise.
Querl nodded. "I too am a black sheep." He explained. "Before you, the Luthors were villains, adversaries, and foes of the heroes we as the Legion uphold as our icons. But you change things, you showed the world and history that not all Luthors were like Lex and Lillian. Even when it must have felt like the most futile thing in the world, you persisted, and I find that far more heroic. I work everyday to show I am not the Braninics that came before me. I want to make up for what my ancestors did, I want to be good, I want to be a hero, but sometimes all people still see is the villain behind my name."
That was certainly something Lena could relate too. Sometimes making a name for herself while repairing the image of L-Corp felt as useless as pushing a boulder up the side of a mountain. It was nice to have the bit of hope Querl was offering that it wasn't all for nothing. "You helped protect my son and you're helping me save my friend. That makes you a hero in my book, Querl."
Querl smiled warmly. "That means a lot coming from you, Ms. Luthor."
Once they were ready Alex came over to monitor Sam's medical readings while Lena maintained the other machines and readouts.
"I will do my best to make this as painless as possible." Querl reassured. "However, we are basically resequencing every strand of her DNA, removing and repairing the base building blocks of her genetic makeup."
Lena and Alex nodded their understanding. Despite the best efforts and their deepish wishes, this was going to cause Sam pain.
"I have always found your coding work quite beautiful, Ms. Luthor." Querl said as he connected himself to Lena's computers and began uploading her programming. "But this is truly a work of art."
Kara brooded quietly in the monitoring room. Was he simply a fanboy or was he hitting on her girlfriend? She wished she could be closer, be in the room with them, but she couldn't. The red sun lighting in the room was on full intensity and would nullify her powers quickly. If something went wrong they would decrease the power of the red sun lights to a level that would allow Kara to step in, and hopefully deal with the matter before the red sun light began affecting the yellow sun energy her cells kept stored up. Kara actually had some experience adjusting to the red sun lights these days. A snapped headboard and two finger splits had inspired Lena to reconfigure the lighting in her bedroom to mimic both red sunlight for when Kara's powers needed to be toned down a little, and yellow for when Kara needed a bit of a charge. So they knew at what level to set the red sun light to if Kara needed to intervene.
Kara watched Brainiac 5 put both of his hands about an inch above Sam's body and then nearly jumped as she watched all ten of his fingers sprout into tentacle like conduits that implanted into Sam at various places along her torso, arms, legs, chest, the back of her neck, and her temples. She moved closer to the screen to see what was happening as a purple pulsing light began running from the cable leading from Lena's computers to Brainiac 5, and then out through his fingers into Sam.
Lena watched the progress on her screen and said, "This is going to take awhile."
"Sam's stable." Alex added. "For now."
Soon after the procedure started the pattern of lights in Brainiac 5's fingers began to change. While some of the conduits continued to pulse purple light into Sam, some of them began pulsing red light towards Brainiac 5. Those red pulses then made their way down another cable connected to a large black hard drive.
"What is that?" Kara asked into the microphone. "The black box? What is it?"
Lena explained. "Querl is removing the Reign code from Sam and then repairing the damage removing it is leaving behind. It needs to be done quickly, instantly, so we're moving the Reign coding to the device which can then be physically destroyed later, so we can concentrate on Sam's needs first and foremost."
"And the code will only be in the hard drive?" Kara asked next.
Lena nodded. "Querl and I made sure he was protected against it before we started."
"Good." Kara replied as she stood and crossed her arms over her chest. The last thing they needed was a Brainiac with Reign programming.
After more than an hour had passed Sam's body began to twitch involuntarily. After three it began to spasm and jerk. Alex continue to report that Sam was stable, but that didn't make it any less hard to watch. Kara didn't like seeing the people she cared about in pain. J'onn tried to reassure them all that Sam was still deeply unconscious and was not registering the pain at all, but who's to say that once this was all over she wouldn't remember it? Sam was going to need a lot of help and support after this and Kara promised Rao she would be there for her cousin. She would help Sam in the way she wished she could have helped her Aunt Astra. Of course that meant she needed her cousin to come out of this alive and well. Six hours in and Sam's body was bowing and thrashing on the table. Kara stood with fists clenched so tightly her knuckles were white.
"Nearly there." Queral said, his voice strained, his body covered in sweat, his coloring changing from soft ivy or shamrock green to pale key lime kind of green.
It took nine hours from start to finish. Querl's knees buckled as soon as he'd detached himself from Sam and the computers, sending him crashing to the floor in a limp heap. Alex had him rushed to the medlab while she and Lena checked Sam over. Alex had been able to isolate Reign's pattern from Sam's on an EEG after pulling Sam's medical records and spending many sleepless nights pouring over data. They would give Sam's body time to recover and then bring her out of her unconscious state just enough for Alex to run the tests again. Any decisions after that would depend on what Alex found.
"Do you think it worked?" Winn asked as soon as Alex and Lena joined them around the command table.
"I hope so." Alex replied while she rubbed the back of her neck. For Ruby's sake she hoped so. Alex had been preparing for the possibility that Ruby would need a more permanent guardian and was more then willing to be that guardian, but what she wanted most for the girl she'd grown to care so much about was for her to have her mother back. That wasn't ever something Alex could have done for Kara, though there were times when she wished she could have, but she was hoping so badly that she could do it for Ruby.
Everyone eyed the hard drive Lena placed on the table. Winn was about to ask what they were going to do with it when they picked up on the faintest of hums just before the device began to melt under Kara's heat vision. When she stopped there was nothing left but a puddle of molten goo. Everyone stared at Kara and before J'onn or Alex could fuss at her for pretty much destroying the command table Winn piped in.
"Lena and I were looking for a reason to build a new one." Winn said brightly. "We have a lot of ideas."
They waited for what seemed like forever before Alex confirmed that to the best of her knowledge there was no sign of Reign. Of course they couldn't be absolutely sure until they woke Sam up and once again waited. They slowly released her from the psychic coma J'onn had put Sam in, and then waited for her to come around on her own. When she did, Lena and Alex were with her.
Sam jolted awake with a gasp as if starling awake from a nightmare. Her dark eyes darted around the room, it's unfamilatry and starkness making the panic worse.
"It's alright, Sam." Lena said gently as she tried to calm the woman. "It's ok, you're ok."
Sam focused on the familiar voice, seeking out it's source. When she finally locked eyes on Lena she relaxed a little. Her voice was horse and it hurt to speak but she managed a rasped, "Le, na."
"I'm here." Lena said gently. "It's going to be alright."
"Just take it easy, Sam." Alex added in, finally drawing the other woman's attention. "You've been unconscious for awhile, let's get you settled and then we can deal with things."
Sam turned her head towards the second voice and the moment she saw Alex she asked, "Ru, by?"
"Safe." Alex reassured. "She's been staying with me. She's safe and sound, and really missing her mom." Tears began to well in Sam's eyes. Alex reached out and put a hand on her shoulder. "I know, but it's going to be ok Sam. Just relax, let us help."
They didn't want to bombard Sam right away but they needed to ascertain whether or not she still had any of the Reign programming. When Sam described the way it had felt, she said it had been like she'd been encased in a cold dark crystal. She could watch what was happening but do nothing more than pound on the walls of that crystal. She would scream and shout and cry out, but be greeted with only silence and the nightmare before her. When asked how she felt now Sam took awhile before answering. "Scared." She admitted. "But I don't feel like there's a monster lurking in the shadows anymore."
The first time Supergirl walks into the room Sam can't even look at her. "It wasn't you, Sam. It wasn't your fault. It was Reign."
"I am Reign." Sam replied with a shake of her head.
Kara reaches for Sam but Sam pulls away. "Reign was a weapon you were forced to carry against your will. She isn't who you are, Sam."
"I almost killed you." Sam said, her voice thick with the tears welling up in her eyes.
"But you didn't." Kara tried to reassure.
Sam pulled her legs up to her chest as if retreating into herself. "I killed Morgan Edge, those boys on the pier, those men…" She froze, her head snapped up and she looked over to where Lena was standing. "Oh god, Lena."
"What?" Lena asked as she came closer. "What's wrong Sam?"
"Your mother." Sam replied, her dark eyes wide. "Lena, I think… I think I might.. I think I might have killed your mother."
Lena honestly had no idea how to react to this. Lillian Luthor was a vile, evil woman, whose sole purpose in life was to kill everyone Lena loved most. Lena hated her. And yet, there was a small part of Lena, the part that had spent the better part of her life as Lillian's daughter who clung to a child's love for their parent, wither the parent was a good one or not. "What happened Sam?"
Sam had to think for a moment. So many of her memories as Reign felt unreal, like scenes from a movie she'd been forced to watch. "I went looking for her and found her in an underground bunker, in Metropolis, under a barber shop. I killed the men she had with her. I had her cornered, she was injured, I was about to… about to…" She paused, her hands flying up to cover her eyes. When she finally looked up at them tears ran down her cheeks. "I heard Supergirl call my name. I flew straight up. I could hear rubble falling behind me. I heard her scream."
Kara reached for Lena's hand and held it reassuringly. "We'll send someone to check it out."
Lena nodded at Kara while speaking to Sam. "I'm sure she survived, Sam. We could face the end of the world and the only things to survive would be cockroaches and my mother."
Kara spent as much time as she could with Sam. She reassured Sam that the team that came back from Metropolis hadn't found Lillian's body so it was a safe bet that she escaped and was out there somewhere fuming and brooding and plotting against them. "It's alright Sam, you didn't kill Lena's mother."
"Lena would have never forgiven herself." Sam said softly. "If she thought she'd somehow sent that monster, sent me, after Lillian no matter how much she hates her. Even if it were indirectly, she would have blamed herself. "
It was a glimmer of the old Sam. She was more concerned with what it would have meant to Lena, not herself.
Kara told Sam they were family. "Our mothers were sisters, twins actually, which were ultra rare on Krypton. They were truly special. My mother's name was Alura and yours was Astra." Kara sighed softly. "If she'd been allowed to she would have loved you so much."
It was important to Kara that Sam know the Astra she knew most of her life not the woman she was at the end, the woman Non had turned her into. Plus, they didn't want to overwhelm her. She was already having a hard time dealing with what she'd done as Reign, they didn't want to add to that the fact that her parents had once been the villains too.
They all knew this would be hard on Sam, that she would need time to heal, to recover and deal with what happened to her. What they didn't expect was for her to flat out refuse to see Ruby. "I was going to hurt her! I was going to kill her!"
"No Sam." Kara said firmly as she watched Sam pace the room. "You saved her! You broke free of Reign's control to save Ruby."
But Sam flat out refused to see her daughter. Even after they made the hard choice to take her back to the fortress. They needed to make sure the Reign programming was gone before the Legion went back to their time. Sam told them that Reign had come out after she'd gone to the fortress the first time. The hologram of the dark priestess raged when she realized Reign was no more. The fortress shook and came down around them. Once they were clear of it they watched as the fortress sank into the ground. Kara watched as Sam walked over to where it once was and retrieved the dark crystal that had created it. She used her strength to dystory it, and then when they returned Sam retreated to the windowless red sun room she'd been staying in since that night. The night she nearly killed her daughter.
"I don't know how to help her." Kara said softly as she dropped her head.
"You'll figure it out." Mon-El reassured. "Trust me on that."
Kara looked up and he was smiling at her. She returned that warm smile.
"It's time for us to go." He said to them. "Sam had been restored, Reign had been defeated, and Andrew's safe from my people."
"Thank you." Kara said. "For everything."
Mon-El smiled, then he turned to Lena.
"You don't have to stick to what you did." Lena told him yet again. "You're welcome to be apart of his life."
"His life is here with you and Kara." Mon-El said softly. Though there was pain in his eyes, there was also conviction. "Mine is in the thirty-first with Imra and whatever future awaits us." He reached into his pocket and pulled out a ring like the one he wore. "I would like to ask one favor of you, Lena." He looked at the gold ring with the L and shooting star on it. "When he's old enough, when you think he's ready for it, give this to our son."
Lena accepted the ring and nodded. "I will, Mon-El, I promise."
Kara stepped up to stand beside Lena. "I'll take care of him, Mon-El."
"I know you will." Mon-El replied. "He's in good hands."
Mon-El stepped onto the disk beside Imra, taking her hand. She reached up to cup his face and press her forehead to his.
"Querl." Kara said as she stepped up to Brainiac 5. She held out her hand and smiled warmly at him. "Thank you. You not only helped save Andrew but Sam as well. You're alright in my books."
Querl smiled a huge smile. "You are welcome Kara Zor-El."
They returned to Lena's penthouse that night and cuddled on the sofa with Andrew. It felt like the first time in weeks since they'd last been together like this. Reign, Lobo, the Legion, it had all been so overwhelming and piled on one thing after another. They hadn't really had time to just sit down, take a breath, and process everything that had happened.
"Do you know why I used Daniel as his middle name rather than just using Danvers?" Lena asked as she watched Kara play with Andrew. The two of them were tucked under a throw while Andrew stood on Kara's thighs, his little hands held in Kara's. When Kara turned to look at her she smiled and said, "Because a part of me always hoped to add Danvers as a second surname."
That got the brightest smile from Kara. Leaning over she captured Lena's lips in a loving kiss. When she pulled away she rested her forehead against Lena's. "I love him as my own, Lena. I have loved him since the moment I discovered he was yours, because I love you."
"I love you too." Lena replied happily.
Alex marched into Sam's room holding her cellphone in her hand. Kara could treat Sam with kid gloves all she wanted but that wasn't Alex's style. Moving a chair over so she could sit in front of the woman sitting on the bed Alex held out the cellphone and said, "Take this and say hello."
Sam blinked. She stared at Alex and the phone with a mix of confusion and fear. "Alex?"
"Take the damn phone, Sam." Alex ordered. "And say hello."
Reaching out a shaking hand Sam did as Alex ordered. Bringing the phone to her ear she whispered, "Hello?"
"Mommy!"
Sam's heart stopped and her eyes were instantly filled with tears. "Ruby."
"You're awake!" Ruby said excitedly, her voice laced with happiness and relief. "She did it! Aunt Lena did it! She saved you!" There was a sobbing laugh and then Ruby said, "Mommy, I miss you! When can I see you?"
"Oh Rubes." Sam sighed as she dissolved into a puddle of emotion.
Alex moved from the chair to sit beside Sam on the bed. She put her arm around the other woman and drew her into her side. She didn't say anything, she simply offered Sam some of her strength and some comfort.
"Ruby, honey, I don't know…" Sam began to say.
"Please Mom." Ruby begged. "I miss you."
Sam covered her mouth to hold in a sob. When she was sure she could speak again she said, "I miss you too, baby."
"Alex said you were afraid." Ruby said. "It's ok to be afraid. It's been really scary lately. But I can be brave for both of us, Mom. I have faith in you, and I can be brave. I'm still not very good at having patience though, cause I just really really need to see you even though I know you're still trying to get better."
Hearing her daughter's voice, hearing Ruby practically begging to see her, how was Sam supposed to ignore that? Sam's heart twisted painfully in her chest with mixed emotions. She was still so afraid of hurting Ruby, but every part of her longed to hold her little girl in her arms again.
"Mom please." Ruby said softly.
Sam had to swallow another sob. "Alright Ruby. Tomorrow, when Supergirl is here, you can come see me."
"I can't wait!" Ruby replied. "I'm gonna call Aunt Kara now and tell her! I love you Mom! I miss you! I'll see you tomorrow!"
When Sam handed the phone back to Alex she turned to glare at the woman who'd been holding her. "That wasn't fair."
"Nope." Alex admitted as she slipped her phone into her pocket. "It wasn't, but you were being stubborn. You need Ruby as much as she needs you. You can find other ways to punish yourself that doesn't involve that kid, because she's an incredible kid and I for one would do anything to see her happy."
Sam blinked. She looked at Alex for a long time as she thought about how this woman who'd just started to become a friend, had stepped up to take care of her daughter. Alex had taken Ruby in, cared for her, was there for her, and maybe even loved her when Sam couldn't. Sam blinked again. "Thank you."
Alex smiled, she even blushed a little under Sam's glare. "Ruby's pretty amazing. She's smart and strong and she gets that from you. You're going to get through this, Sam."
If only Sam could believe that.