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Disclaimer: I do not own anything. Just having some fun.

Rating: T (Subject to change later on. Will let you know though.)

Note To Readers, 23rd August 2014: I've decided to write this story in a sort of episode format. So each complete chapter which will normally have more than one part will make up an Episode. At the beginning of Each new Chapter/Episode i will write out a quick Summery as well as list the main Characters for it.

Note to readers:

So first up I am going to tell you that Clark/Kal and Kara are an item. Now before anyone goes off about the whole kissing cousins thing, I would like to explain where this idea came from.

In the DC Animated universe, Superman TAS and the Justice League Cartoon Series, Clark and Kara were not related in any way. In fact Kara wasn't even from Krypton, she was from Argo which was Kryptons Sister Planet. That is where some of the ideas for this story come from.

In the Smallville Series, Kara's 'Father' Zor-El treated her like crap. In fact he seemed to treat her as an object that he controlled (Much like Jor-El did with Clark mind you). So anyway i started thinking about some reasons why Zor-El could possibly treat Kara the way he did. It was when i was doing some research into writing this story that i came across the Animated Version of Supergirl, who's name was actually Kara In-Ze.

So the concept in this story of Clark and Kara being together is based on her actually being Kara In-Ze instead of Kara Zor-El. However to keep within the Smallville continuity i came up with a reason why Kara was raised by Zor-El instead of In-Ze.

I will be giving some details on this in the prologue so after you've read it you can decide if you wish to continue doing so.

On another note i have not been reading the Smallville Comics but will be referencing the Smallville Wikia. I will also be Referencing the DC Universe in general which includes the New 52.

So getting back to my original point in this little Note. Kara in this story is not biologically related to Clark/Kal..

Chapter 1 Summary: In the 33rd century a strike team is sent back in time to kill the members of the Justice League before it's even formed. To counter them, Kal-El travels back in time to just before the second Meteor Shower in hopes of resetting the timeline and building a brand new future. (Clark/Kara. They are not biologically related in this story. See above for Explanation.)

Chapter 1 Main Characters: Clark Kent/Kal, Linda Danvers/Kara, Jonathan Kent, Martha Kent.

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Through Eternity

Volume I:

Prologue

=August 3227=

"So how many went through?" Kal who was known throughout not only this galaxy but several others asked as he looked at Kara who was now wiping away tears from her eyes.

"I don't know." Kara answered honestly. She'd had to hit top speed to get to the Fortress before the timelines shifted. She'd got within the Fortress shields just in time to literally watch the world around her change. She knew without a doubt that the world that was currently outside was not the world she had just left. "How are the shields holding?" She then asked.

"They're still holding pretty strong." Kal answered as he walked up to her and placed his hand gently on her shoulder. "There's been six shifts in the timeline already. Whatever is happening, it's bad."

"I don't know how many went back, but I managed to find out when they've gone and what they were planning." Kara said as she looked up into Kal's eyes. "They've gone back to destroy the League before you all went public. It looks like they've gone back to the summer of 2007."

Kal took a step back from Kara and closed his eyes for a few seconds. He'd always feared this day would come as he had encountered a few people from the future that had gone back to kill him while he was a member of the League. For him it had been over twelve hundred years since he first went public and the Justice League became truly active.

Opening his eyes again he turned his head towards the main control crystal in the centre of the fortress. "Father!" He called out.

"I am here my son." The disembodied voice of Jor-El answered.

"I need you to run a complete scan of the timeline ranging from 2006 to 2026. I need to know where the first shift in the timeline took place." Kal stated with a firm tone.

"Kal, what are you planning?" Kara asked.

Kal turned back to Kara and looked at her with sadness in his eyes. "When the last shift in the timeline happened, I scanned the Earth to see what's changed. The only reason you weren't effected was because of your Legion Ring. But it's bad, really bad."

Kara again looked into Kal's eyes and she could see for the first time that he was holding his emotions back. "Kal?" She questioned with a little fear in her voice.

Kal shook his head sadly and let out a deep sigh. "There's nothing out there. No life at all. The Earth is completely barren."

Hearing those words coming from Kal, Kara stumbled back in both shock and horror. "No!" She whispered in disbelief.

"They... They're all gone." Kal said again while struggling to hold his emotions in check.

In that moment, Kara's entire universe seemed to fall apart.

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Several hours later, Kara awoke and the first thing she noticed even before opening her eyes was that there was nobody else in the bed. Opening her eyes she looked around for Kal only to find that he wasn't there. They'd been together now for just over a hundred years and it had been the best century of her life. She'd often find herself thinking back on when he'd first returned after being away for nearly nine hundred years. He'd left Earth after being Superman for nearly two hundred years deeply depressed by the constant losses of those around him. After being in the future herself for nearly a century, she began to understand why he'd left.

When she'd returned to the future after Kal had helped with the incident involving New Krypton, she'd been welcomed back with open arms. She'd taken it upon herself to carry on Kal's legacy. However after nearly a century she understood why Kal left. Being Kryptonian on a planet with a yellow sun made her essentially immortal. She looked the exact same today as she did over two hundred years ago from her perspective. It was hard and painful to watch all those she loved whither away and die.

She was in fact going to leave Earth for New Krypton when Kal returned to Earth in 3116. Even now she still remembered that first day when he arrived at the Fortress. His eyes were so worn, so full of pain and loss that she almost burst into tears just by looking at him. Even he hadn't changed at all from the last time she'd seen him in the 21st century. The look in his eyes completely shattered her heart.

When Kal had returned to Earth he was happy to see her, but he kept himself emotionally distant from her. He often reminded her of those blasted council members back on Krypton before the fall. She knew that he'd spent those nine hundred years alone just wandering the universe. It took nearly six months for her to get him to finally open up a bit. What she had learned had shaken her to the core.

Kal was essentially an illegal birth on Krypton. In fact at the time as far as she knew he was the first naturally conceived child on Krypton for several centuries. She knew that Jor-El and Lara had broken the law in conceiving Kal naturally but she was young and happy for her 'aunt' as she knew that both Lara and Jor-El didn't agree with the birthing matrix. They'd both always said that growing children wasn't natural and was holding them back a species. It turned out that they were right.

When she'd managed to get Kal to finally open up he told her a few things. Because he was a free birth there were a few subtle differences. He was stronger and faster than any other Kryptonian and his body absorbed solar energy more efficiently. His body had changed so much over the centuries that even the light of a red sun didn't take away his powers. No matter where he went he still had the powers that he had on Earth. Because of this and the knowledge that he was going to pretty much live until all the stars in the universe die out, he'd fallen into a state of deep depression.

Kara had always known that Kal feared one thing above all else, being alone. While she had that same fear, she had the option of going to New Krypton and becoming mortal. However much to her sadness, Kal didn't have that luxury.

Breaking herself away from those thoughts and memories, Kara kicked the sheet off herself and stood up. As usual she was completely naked as she always preferred sleeping in the nude. She remembered Kal lecturing her when they first met about not wearing clothes the bed. It was a completely foreign notion to her, but she understood that on Earth things were different.

Not even bothering to put anything on, Kara walked out of the bedroom in the Fortress to look for Kal. It took her only a few seconds to find him and he was sitting in a chair in front of the large computer looking over some data that he was collecting.

Walking up behind him she reached around the chair and wrapped her right arm across his chest. "How long have you been up?" She asked softly as he brought his own hand up to cover hers.

Kal took hold of Kara's hand that was on his chest as he looked up at her. "About an hour." He answered. "Jor-El and I have been talking over a few different ideas. We've got one that might work, but there's a problem."

"What is it?" She again asked softly while gazing into his eyes. She knew he was troubled by whatever he and Jor-El had been talking about.

Kal let out a small sigh before answering. "Jor-El thinks I should go back in time to just before the Fortress was built. He thinks that by going back way before those things get back, I can change the timeline in a way that they would never have existed in the first place to be sent back."

Kara stood there leaning against the back of the chair thinking over what Kal had said. She had to admit that Jor-El was right in his assessment. While she hadn't studied the complete archives of the fortress, she had studied a lot and knew a fair bit about time travel. "That could work. I mean if the timeline is altered before they even go back, then they would not exist to be sent back in the first place... " Whatever she was about to say beyond that though was cut off by Kal.

"If i do this, you cant come back. Your younger self's body is still in stasis in your ship. I wont be able to send your consciousness back." He said interrupting her.

Hearing Kal's words, Kara suddenly realised that he was right. Being in stasis, he wouldn't be able to send her consciousness back into her younger body. If he went and got her from her ship, she would have no idea of who he was. On top of that, she would also not know the truth of who she really was. "There has to be something that we can do." She finally said although this time there was a little uncertainty in her voice.

Kal looked up at Kara for a second before standing up and taking hold of both her hands. Once on his feet the first thing he did notice was that she was completely naked, not that he minded. "I'll figure something out Kara, I promise." He said before reaching up under her chin and tilting her head towards him. "I wont loose you again." What Kal said was true and he didn't think he could cope with loosing everything that he and Kara had become over the last century.

It was no secret that when he returned from his journey amongst the stars that he was heavily depressed and detached from the world around him. He'd seen so many of those he loved whither away and die that he was loosing himself in grief and loneliness. Despite Kara wanting to return to Argo, she had stayed with him and helped heal his heart and soul. It wasn't however until after Brianiac had told both himself and Kara the truth of her heritage that things really began to change.

While Kal was lost in his thoughts, Kara was lost in her own. She knew that Kal had to go back in order to protect the Earth. She'd seen the sensor data on the state of the Earth and it was now a lifeless rock. There was no other way and she knew it. She also knew that Kal knew it as well. "You have to go back." She finally said with true sadness in her voice. "You know you have to."

Kal pulled Kara into a tight hug and closed his eyes knowing that she was right. As for Kara she wrapped her arms around his waist and rested her head against his chest. "I'm sorry." He finally whispered as he opened his eyes. "Jor-El. Make the Crystal that's needed for our plan." He ordered knowing that Jor-El was already prepared to make it.

"It will take several hours for the crystal to be formed and prepared for your journey into the past." Jor-El said. "I am sorry Kara."

"I know," Was all that Kara could say back to Jor-El before opening her own eyes and looking up into Kal's. "Take me to bed." She whispered. "Let's spend what time we have left together."

Kal looked down at Kara before nodding his head. "I love you."

"Forever." Came the simple response from Kara before the pair headed back to their bedroom.

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=May 2005=

Jonathan and Martha Kent were pacing back and forth in a worried state. Half an hour earlier, Clark was doing some work out in the barn when he suddenly screamed out in what sounded like pain. When they arrived in the barn they found him on the floor unconscious and hadn't been able to wake him.

"I cant believe this is happening again. What's Jor-El doing to him now?" Martha said in anger as she had no doubt that this was Jor-El's doing.

Jonathan stopped his pacing and moved up to his wife. "I'll give it half and hour and then I'm going to the cave. I wont let Jor-El harm our son anymore." He said firmly.

"Jonathan, you cant. You know what happened last time you confronted him." Martha reasoned. Despite her fear over what was happening to Clark, she knew that Jor-El would not physically harm him. "Jor-El wont hurt him."

"Maybe." Jonathan conceded. "But I remember what you and Clark told me about Kal-El. What if Jor-El is trying to bring him back?"

Martha didn't have an answer for that. However she did know that the only thing that worked last time was the black kryptonite. It had been a close call then and she hoped that it wouldn't be needed again.

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=August 3227=

Kal looked down at Kara with a small smile on his face as he watched her sleep. The last few hours had been filled with an intense passion that he could never put into words. Sex with her had always been that way and it was something that he'd never forget. It was always powerful and intense that left them both feeling like a star about to go nova.

He'd never actually told Kara this but Kal had been devastated when she told him that they were cousins when they first met. After his first encounter with her, he wasn't ashamed to admit that she aroused him easily. She stunningly beautiful and the moment he laid eyes on her a part of him wanted her. However all that changed when she said that their fathers were brothers. Even now he remembered the way he'd stumbled back in shock as she told him. Part of it was the shock that he actually had living family, but there was another reason. He'd been shocked by the fact that he was turned on by his cousin. He knew that he shouldn't have been ashamed of his reaction to her back then. They didn't know who the other was back then. However for the next few days he'd kicked himself a few times for his reaction to her.

As Kal came out of that memory another popped into his head. It was the last day that he and Kara saw Brainiac before he left for New Krypton. They'd needed his help so he'd agreed to go with them. That was just over a century ago.

=Flashback.=

"So are you ready for this?" Kal asked his friend as they waited for the Kryptonian ship to land.

Brainac 5 turned to his 'friend' and nodded his head. "Your Father built me to help Krypton and i failed. While i can do nothing to change that, i can still help what is left of your people."

"Our people." Kal corrected. "They are your people just as much as mine."

"You've always treated me fairly Kal-El." Brainiac said as he looked at Kal-El. "Considering my history with you. I did not expect you to be so friendly. I am glad that i was wrong."

"I've been alive for over a thousand years my friend." Kal said with a sad smile. "I learned a long time ago that holding grudges is pointless. Your not the same person you were back then."

"I have learned much in my time here. And through you and Kara i have learned what friendship and family truly is. It is not something that i had expected to learn, or understand."

"Life's funny that way sometimes." Kal responded and before he could say anything further he heard Kara speak as she joined them.

"I never thought i'd say this." Kara began with a smile. "But i am going to miss you Brainiac."

Brainiac tilted his head to the side slightly before responding. "I will 'miss' our time together as well." It was then that he stopped speaking for a second as he looked at the last two true Kryptonians in the Universe. While the others on New Krypton were technically Kryptonian, they were beginning to evolve in a different path. Within the next few thousand years, they would no longer be Kryptonian but a new sub-species.

While he was looking at the two Kryptonians, Brainiac decided he needed to tell them the truth. Which was also something that Jor-El had asked was never revealed to them. However with his understanding of organics that he'd gained over the last century or so, he decided that he should disobey that order. Both Kal-El and Kara needed to know. "There is something that you both should know. It is something that Jor-El ordered me not to reveal to you." Then he focused his full attention on Kara. "It will also explain why Jor-El wanted you to leave Kal-El when you first came here from the 21st century."

Both Kal and Kara glanced at each other before turning their attention back to Brainiac. "What is it?" Kara asked.

Brainiac focused on Kara and began to speak. "You once told me that when i trapped you in the Phantom Zone, that you could have easily escaped. You told me that Zor-El built a back door access for you in the portal system." He said which got him a nod from Kara as well as a look of confusion. "You would not have needed your own back door to the portal if you were a member of the house of El. Jor-El had already built in a failsafe to protect his family should any of them be trapped there."

Both Kara and Kal understood what Brainiac was trying to say, yet they didn't understand the point. "What are you getting at?" Kal asked.

"The only reason you would need your own back door access Kara." Brainiac began but stopped for a second. "Is if you were not an El."

"What!" Both Kara and Kal said at the same time equally as shocked as the other as the implication of what Brainiac was implying sank in.

Brainiac was fully expecting such a response and give them a few seconds to process things. After a few seconds he decided to carry on speaking. "When you told me about the portal i became curious as to why you'd need your own access. I went to Jor-El with my theory that you were not a member of the house of El. My own scan of your genetic makeup had already confirmed my suspicions." As he was talking he could see that both Kal and Kara were in a state of shock but continued his story. "I confronted Jor-El and after a rather lengthy debate, he confirmed what i had discovered."

"I... I'm not an El?" Kara stammered in shock and confusion.

Kal despite being just as shocked as Kara could see that learning this was hard on her. However he also knew that she needed to hear this, and so did he. "Why didn't you say anything sooner?" He asked.

"As i stated earlier. Jor-El ordered me not to." Brainiac answered to which he got an annoyed look from Kal that he knew all to well. Kal had said many times in the past that Jor-El's approach to things drove him to anger many times. "Jor-El was afraid of what would happen should the two of you learn the truth." He then said calmly.

"I don't understand." Kara said still with shock in her voice. "If I'm not an El, then what am I?"

"You were not born into the house of El. Zor-El and his wife took you into their care after your parents were executed by order of the council..." Whatever he was about to say next was interrupted by Kara.

"What? What do you mean executed by the council?" Kara asked now even more confused than she was before. Kal for his part had to agree with her.

"You and Kal-El have one thing in common that no other of the Ancient Kryptonian race have. You were both naturally conceived and born." Brainiac answered truthfully. "Your biological parents violated Kryptonian law and naturally conceived a child, that child was you." He said gesturing towards Kara. " However unlike Lara and Jor-El, they did not cover their 'tracks' as humans say very well and the truth was discovered by the council." From there Brainiac went on to explain that after Kara's birth, her parents were arrested and tried for violating Kryptonian law. Each child on Krypton was engineered to fulfil a function within society and a free birthed child was not part of the 'plan'. "The council found your parents guilty and ordered their execution. However Kryptonian law prevented them from having you killed. A child cannot be held responsible for the crimes of it's parents. As a result, you ended up being raised by your biological father's sister. The woman you knew as Allura In-Ze."

Both Kal and Kara's minds were reeling over this revelation. Neither of them knew what to say or do at this point. Everything that both of them had been told in the past was turning out to be a lie. It was not something that either of them could easily accept.

For the next few minutes nobody spoke and Brainiac give the pair time to allow his revelation to sink in. After nearly five minutes Kara finally spoke. "Who were my birth parents?" She asked with a shaky voice.

"If the information that Jor-El provided me is accurate. Your Mother's name was Kala Im-Re and your Father's name was Zor In-Ze. Your mother was an astrophysicist and your father a teacher. You were born Kara In-Ze."

=End Flashback.=

Kara suddenly bolted upright breaking Kal from the memory of that day. "Kara?" He questioned.

Kara was panting slightly and it took her a few seconds to calm down. Once her mind settled down she turned her attention to Kal. "I've got an idea." She said with a smile on her face before she leaned in and kissed Kal quickly on the lips before jumping out of the bed.

Kal's gaze just followed Kara's naked form as she quickly made her way out of the room. After a second or two, he shook his head and got up to follow her. Making his way into the main lab he heard Kara speak.

"Jor-El, i've got an idea i need to run past you."

The tone in Kara's voice made Kal realise one thing. Whatever this idea was, he was going to like it.

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So there's the prologue. Hope you like.