Chapter 23

Pepper stirred her newly prepared coffee – the fourth one she would have today. Her father and Marsha were watching television in the living room, and the redhead had practically been hiding in her room all day. Well, hiding was not the appropriate word. If it came down to it, she was merely pulling a Tony Stark.

Ever since the results of Reed Richard's tests had landed in her e-mail this morning, she had been working nonstop to use them to prove to Tony that he had not caused the car pileup. On his end, Tony was using the tests Reed had ran on Pepper to prove to her that she was not losing her humanity or gender, and that he could find out a way to get them both back.

She dropped the used spoon in the dishwashing machine and ran it, knowing that after she finished this cup she was due to sleep, anyway. It was nearly midnight on a Sunday, and she had to show up for her final driving lesson the next day, as early as 7 AM.

I'm so gonna wing it, the ginger thought as she walked out of the kitchen and headed to the stairs. Her father spared her a worried glance, seeing how much she had been working in the past few days, but he understood that she and Tony were trying to iron out – no pun intended – the consequences of Pepper's disappearance.

Truth be told, he was surprised they were still together, seeing as how Pepper had tried – and had almost succeeded – to kill him nearly six weeks ago, and how much trouble she had caused to him and the scientist's father and family doctor. He had no idea their feelings could be so resilient at such a young age, but he also remembered that at some point he and his late wife had been like that as well.

It must be love, the FBI man thought before he returned his attention to the movie once Pepper was out of sight.

The girl yawned loudly as her feet dragged on the wooden floors all the way to her room. Just as before when she had returned from pouring herself more coffee, she closed and locked the door behind her, walked directly to her workstation, and sat in the same swiveling chair she had been attached to since four in the morning today. Her Stark Pod was shining brightly next to her electronic table, letting her know that she had missed a text or a call.

She placed her cup of coffee on the table next to her other three cups, and then proceeded to grab the cell phone. She smiled widely when she saw Tony had sent her a text message, telling her how much he missed her and she responded that she missed him, too. They had not seen each other since the outing to the Baxter building, simply because the both of them had been so dang busy with their chores.

The phone lit up again almost instantly with another text message from the inventor, this one containing a picture of him holding a piece of paper asking her to go out on a date next weekend. She responded with a smile and a kiss, and Tony responded with a 'heck, yeah.' Everything seemed to be returning to normal – whatever normal meant for them, and she was so glad that she had listened to Tony's request to try working out the kinks one last time.

The only thing she feared, however, was that this moment of peace was just the calm before the appearance of a thunderstorm worthy of Thor.

Her eyes returned to her monitor and she took a sip of her coffee as she ran another simulation of Tony's Extremis virus. Thanks to Reed's advanced machines and test results, she had been able to create an algorithm that was able to read certain waves that Tony emanated when calling onto his Extremis powers, particularly when he tried to access and hack into computers. Her goal was to match these waves and their actions to how the traffic light algorithm had been affected to see if Tony's virus had actually had any involvement in the accident.

At first, the simulations of the virus he had infected himself with appeared to have had no discernable pattern. However, the more simulations she ran, and thanks to JARVIS' help, they had been able to see that the pattern pertained to how each computer was affected by Tony's will, rather than Tony's hacking always attacking the programming in the same way.

"Your virus is as complicated as you are, Mr. Stark," she told herself with a smile and set down her coffee. She entered the sequence's commands to run yet another simulation and stretched herself in her chair, eyeing the counter on the computer to realize this particular simulation – one that most resembled the traffic light algorithm, was going to take five minutes to complete.

As she waited for the simulation to be finished, she stared at her charm bracelet. Despite Tony's claim that EMF sensitivity was unproven, her hallucinations had disappeared when she had begun using the charm. The possible side effects of EMF did match the feelings of dread she had experienced the times she had seen Gene, and as Dr. Yinsen had pointed out, the hallucinations did occur only in her or Tony's home.

Her thoughts then shifted to her own theories about Gene and the diadem, which sadly made more sense than EMF. What if the power of the diadem was being confused with EMF? What if it was just a coincidence that she had not seen him anymore while she was wearing the bracelet? What if he was just lurking in the shadows waiting for the perfect moment to strike?

What if she was slowly turning into Gene himself?

Pepper glanced at the countdown on the monitor, which showed two more minutes were needed for the simulation to end. Many things could happen in two minutes; two minutes was a very long time. It had only taken two minutes for Axonn to take her; it had only taken two minutes for Gene to take away something precious from her.

It had only taken two minutes for her to turn on Tony and nearly end his life.

I just have to know, the redhead thought and removed the charm bracelet from her wrist, holding her breath as she waited for the worse to happen. She felt a shiver run down her back and the hairs on her neck stood, but she remained calm. She then twirled in her chair as she had done so many times before, and stared directly at her dark room.

The only light around her was coming from the computer screen, and even her blinds and curtains were closed, preventing the eerie light of the moon from filtering through. She slowly eyed every corner of her room, making several passes on it just to be certain that she was still alone.

"JARVIS?"

"Yes?"

"What are the current EMF readings here?"

"Negligible, Miss Potts."

"What's negligible?"

"0.5"

"What were the readings the night Gene appeared to me in the kitchen?"

"10.5"

"What about the night he was here in the room?"

"12.5"

"And what about when Tony came home late that night after meeting up with Reed?"

"15.5"

"And the night I went cuckoo in the shower?"

"30.2"

"Interesting," she mused. "Can you produce EMF?"

"Yes, but it is against Mr. Stark's orders."

"But you can?"

"Yes, if it is necessary."

"Would it be considered necessary for a science experiment?"

"That could qualify as necessary."

"Get it ready," she ordered. "I'll tell you when to start."

The beeping of her computer startled her until she realized it symbolized the simulation was completed, and she casted aside her current doubts and fears to analyze the results.

"What do we have here?" Pepper asked herself and leaned closer to the screen, staring at the familiar pattern that appeared on the monitor. Her hand flew to her mouse and she cleared her desktop so that she could access previous saved files of Tony using the Extremis. She pulled up the data on those cases and compared them to what she had extracted just now. She narrowed her eyes at the results, and something inside of her stirred, as if her mind was trying to tell her that she had seen these new patterns before.

She rested her head on her upturned right hand and tapped on the table with her left fingers as she stared into space, forcing her mind to pinpoint where she had seen an algorithm like this before. She knew it had been a long time ago since her recent memory had been almost impeccable thanks to the wonders of Axonn's gifts for her. She would have much rather kept the strength and agility she had displayed under her schizophrenic episode, however, but beggars could definitely not be choosers.

"It's just too precise," she mused as she stared at the results on the screen. "Too precise to be human made."

At her words, her fingers suddenly stopped tapping and her eyes widened in shock. She was aware that she was tired as hell and could be very well drawing at straws at this point, but as she had said before, she became more alert under pressure.

"It can't be," she whispered and swallowed hard as her hands returned to the keyboard to pull up information from the archives. She clicked and typed like mad until the particular file she was looking for was pulled up. She then extracted similar data points to run another simulation and waited nervously for the results.

"Please don't let it be this…please, please…don't…"

She cracked her knuckles and then eyed her Stark Pod, grabbing it with trembling hands to be ready to give Tony the warning she feared she had to give. The simulation still had three more minutes to go, so she concentrated on thinking of an action plan to implement in case her theory proved to be true. If it were true, Tony Stark was never responsible for the car pileup, or the EMF wave increase, or…

"The blackout," Pepper said in a low voice. "The blackout was no accident…it was a…"

"Miss Potts?"

"Yes?"

"I'm sensing a stressing increase in your vital signs, are you alright?"

"I…" Pepper swallowed the knot on her throat. "I'm not sure, JARVIS."

"Would you like me to contact Mr. Stark?"

"No. No, I'll call him…right now…" she added the last bit as she slid open her phone and dialed Tony's number. Her eyes were glued to the last minute of the simulation and waited for the phone to ring, but after ten seconds of no sound, Pepper pulled away the phone from her ear and stared at it.

"No signal?" She scoffed. "Why the hell don't I have any signal? JARVIS? Can you get a hold of Tony?"

"One moment, please." The AI responded and it went silent for what seemed like an eternity to the redhead. She was about to call out to the AI again but he spoke up first. "It appears we have lost connection with the server, Miss Potts."

"Tony's server, why? Can you reroute through the satellite?"

"The satellite appears to be offline as well."

"What? Why is the satellite offline?" Pepper began but when she heard the beeping of her computer again, her eyes showed her what she had not wanted to see. "Oh, no…he's alive…he…he's here…JARVIS! Tony, we have to warn him!"

"I…" The AI hesitated. "Error…Miss…Potts…error…type II…"

Pepper stood up from her chair and looked at the ceiling, her heart pounding loudly in her temples. "JARVIS, hang on! Don't…is he with Tony? Is Tony in danger?"

"Miss Potts…error…" JARVIS repeated. "Communication error…commencing emergency lockdown sequence…initiate protocol….3….8…9…"

"NO!" Pepper screamed and ran back to her computer, keying on it like crazy as she tried to prevent what she knew was happening. It could not end like this, not when she had finally figured out what was wrong; not when she finally knew who was responsible for her and Tony's misery. After a few seconds of helping JARVIS reroute himself to host on the server in her house, the AI returned to full function long enough to speak words that left her cold.

"There is another system."

"JARVIS?" her voice almost broke.

"There is…another system. Unable to…t-t-to-o-o…"

Pepper's eyes landed on the red computer screen, blinking and mocking her inability to prevent the final wish of the undercover assailant of her life. As she took in deep breaths and the monitor informed her that the emergency lockdown had failed, she heard the dying voice of the faithful AI echoing in the now dangerous home.

"There-e-e-e…is-s-s-s an-n-nothee-e-r-r-r…s-s-s-ytem-m-m-m…"

The house went dark.

xxxXXXxxx

"Heck yeah!" Tony replied to Pepper's text and set down his pod before returning his attention to the computer screen. He had great news for the ginger, which involved a possible cure for her chromosome issue, and he was excited about letting her know of it during their date. Now that he thought about it, they were due for a real date that did not involve anyone else but them, as everyone and their mother seemed to always end up crashing their attempts at having a normal teenager outing.

"We are not normal, though" the inventor reminded himself. "If we were normal, it would be so boring," he chuckled.

Then again, some normalcy never hurt anyone.

Yet.

"JARVIS, let's call it a night," he stretched his arms above his head and yawned. "Power down everything but keep monitoring the DNA simulation for Pepper's cure, and wake me up at eight."

"Are you certain that only five hours of sleep will hold you up through the day? You do have to meet with Mr. Stark Sr. at 12 PM to review the annual income reports for Stark Solutions."

"Ugh, darn it! I forgot about that. Make it ten, then," the inventor amended his command and stood up from his chair and headed in the direction of his room.

"Will do, sir. Initiating powering down se… que…. initiating… initiating…"

"JARVIS?"

"Sequence…failed…restarting…alert…"

Tony stood in place and stared up at the ceiling with furrowed brows for a brief moment before he walked up to his main computer again and pulled up the current status and specs for the server where JARVIS was hosted. He could see the AI trying to comply with its creator's request, but he was being incredible unsuccessful thus far for a reason unknown.

The boy then pulled out his pod from his pocket with the intention of contacting his girlfriend to check if JARVIS was also malfunctioning on her end and ask if she was again meddling with its code or perhaps running backups of it, but when his call did not go through, Tony just knew something else was at play. "What the hell? Why is our satellite offline?"

"Communication error…type…type…" The AI tried its best to relay the message, but it was having a difficult time doing so when his power sources and databases were being tampered with by outside forces. "Mr. Stark… initiating… lockdown… emergency… protocol…"

Tony pulled up his virtual keyboard and began running his own investigation to determine why his ever trusty AI was failing him, and in the process of doing so he saw an incoming report that left him breathless. Not wanting to jump to conclusions, he first worked his magic to provide the AI with some assistance to pull itself together, all the while staring at the little blinking message on the bottom right corner of his screen.

"JARVIS, you there?" Tony called out when he completed his backup sequence. "JARVIS, are you online?"

"Rebooting."

"What? No! No rebooting!"

"Rebooting."

"Damn!" Tony's attention shifted to the message he had been partially ignoring for the last minute, and when he opened it up, his heart stopped. Before him, in bold, red letters was a message that stated that the Potts' residence had been compromised.

Compromised. He never truly liked that word.

"What is going on?"

Tony ran toward his backup computer to check up on the Stark Solutions satellite firmware, loaded it and tried his best to restart the uplink. After three unsuccessful attempts, Tony was left with no other option but to put on his suit and fly to California himself. He closed his eyes and called upon his armor, and what should have taken less than ten seconds to complete never actually occurred.

The inventor opened his eyes again expecting to see his suit covering every inch of his body, but instead he saw the lights had gone out in the temple and the suit had not even attempted to come to him. He waited in place for a minute for the backup generator to kick in, but when it did not, the genius felt something was very, very wrong.

"JARVIS?"

The silence that followed his statement left him frozen in place for another minute until the familiar buzzing of his systems coming back online was heard. The lights turned on again and the computers began to restart. He took small steps toward his server, staring at it with cautious eyes, even getting the feeling that he was being prowled by it somehow. Using his Extremis gifts, the inventor began taking a virtual peek inside the system. His mind raced as it broke down every piece of code line inside, searching for the malfunction that had nearly caused his entire operating system to short circuit. He expected a virus or an infinite loop to be the culprit, but when he found what he was looking for, it was much worse than expected.

Once found, the assailant fought back.

Tony felt the virtual attack to his brain like a bolt of lightning, pushing him off his feet and sending him flying back and hitting his worktable, causing a mess in the process. He was quickly engulfed by his tools and blueprints, some of which were digging themselves in his back and causing a ridiculous amount of pain.

"JARVIS!"

"Initiating emergency lockdown sequence. Intruder alert."

"No shit!" Tony spat as he pulled himself up to a sitting position on the floor, shook his head, and then stood up from the broken worktable. He again tried calling on his Mark III armor, and when it did not work again, he tried calling on any suit that would respond; any protection was better than none. The result, however, was the same: none of his suits reacted to his command.

But they reacted to his.

I have to get to Pepper. I have to get to her right now.

The sound of the chute locking down and the temple going into emergency lockdown made the situation just that much unnerving to the inventor; he was now trapped in his home, and he was not alone.

"There is another system," the AI spoke up.

"What?"

"There is…another…system…cannot…override…compromised system…error…"

"JARVIS, initiate protocol 389."

"Un…un-n-n-a-ble-ble…"

"JARVIS?"

The lights went out again, but this time the main computer screen remained on, showing to Tony the face of the intruder in his lab. If the inventor ever had wondered what a face of utter fear looked like on him, this was the best time to snap a picture of it while he stared back into those angry, familiar, piercing eyes.