489 A Clean Sweep Conclusion - The Protagonist System - NovelsTime

The Protagonist System

489 A Clean Sweep Conclusion

Author: Bokuboy
updatedAt: 2026-01-12

Persephone needed a moment to let the shock of the man's audacity fade. Did he really think such a simple request would melt her cold heart and allow him entry? She had been alive for centuries and no amount of charm could sway her attitude.

However, that was not true of her cheating husband. He used his charms to manipulate many women over the years and he assumed that any charm sent her way would also easily sway her into the arms of another man. She was not that shallow nor that gullible; but, he thought she was, even after all this time. So, a little teasing was in order.

For the next ten minutes, she regaled the dark haired young man named Atlas about her boring day and she was surprised that he actually listened and was paying attention. Most people only paid lip service to the answers when they asked questions like that. When she finished talking, he shocked her again by what he said.

“It almost sounds like you're a prisoner in gilded cage.” Atlas commented. “It might be great, or the best life you've ever lived; but, you have no freedom to do what you want.”

The Merovingian made an angry sound from the back of his throat.

“When was the last time you went for a walk? Saw the skyline? Enjoyed the company of someone that wasn't fully vetted by the men guarding you?” Atlas asked as his thumb lightly caressed the back of her hand.

“You mean someone like you?” Persephone asked, since it was obvious he was trying to romance her. She wasn't going to fall for his tricks, though. His kind of arrogance was never to be rewarded, especially in a setting like this.

Atlas laughed and shook his head. “No, not me. I'm spoken for.”

Persephone frowned slightly before she could stop herself and pulled her hand out of his.

Atlas didn't seem bothered by that, probably because he had tried to let it go before and she hadn't let him. “She's becoming a lively and fiery woman that might be angry with me if I dared to liaise sexually with someone that wasn't her.”

“Then what are you doing here if you aren't trying to lure me into bed?” Persephone asked and felt a little angry at being played, even if it was her own misconception that made her think along those lines.

“I thought I was offering you friendship that had no strings attached.” Atlas answered and saw the anger she tried to hide. “It seems you aren't going to accept, even if the offer was genuine.”

“You dare to offer me someone else's companionship?” Persephone asked, incredulous. “Who do you think you are to come in here and insult me so?”

The guards at the table off to the side of the raised table stood and looked ready to fight. The Ghost Twins stayed seated, since they thought the man was only a human and the vamps and werewolves would be enough to handle him.

“Are you really so ingrained with the Merovingian's protection that you can't see an offer to escape when it's right in front of you?” Atlas asked, quite pointedly.

They all stilled, even the Merovingian, then a wave of energy passed over everything.

“Well, it doesn't matter now. That's my cue.” He said and dug out two dolls from his pocket. He then stood, quick as a flash, and the two dolls grew to full human size as he flung the one with a long silver bar stuck in his head at the group of standing guards, and a mummified corpse at the Ghost Twins.

The bar skewered one of the werewolves and killed them as the heavy body knocked all of the standing guards down. The Ghost Twins caught the mummified body and the momentum knocked them out of their chairs. They went incorporeal for a few moments before they stood and resumed their solid forms and drew their guns. They couldn't fire with the Merovingian in the way, however.

Persephone could do nothing but stare as the dark haired man leapt towards the downed guards and pulled out the pipe, then he swiped his hand across it and made it into a bright gleaming silver broadsword. With a single swipe, he killed the three vampires by decapitating them, since they were struggling to stand at the same time, then he plunged the blade through the heart of the last werewolf on the floor.

“You will pay for your insolence!” The Merovingian shouted and then gurgled as the man lunged at him and the sword was shoved through the ancient vampire's mouth and out the back of his head.

“Shut up.” Atlas said and did a jumping swing kick and the sole of his expensive shoe kicked the hilt, which was also silver, and the top of the Merovingian's head popped right off as the sword was flung through him and embedded into the wall behind him. It would have hit the twins if they hadn't gone incorporeal.

Of course, this was when everyone in the restaurant noticed the blatant and very public murders happening right in front of them. Most screamed, everyone panicked, and a few of the smart ones tried to leave through the entrance. When they opened the large double doors, it was bricked up.

“No!” Persephone gasped. She was trapped!

The Ghost twins now had a clear shot and opened fire on Atlas, even with her right there. Their automatic pistols unloaded their deadly fire at both her and Atlas, only none of them reached her. If Persephone hadn't been as old as she was, or had her skills, she wouldn't have seen his hands blurring as they caught each and every bullet.

“My turn.” Atlas said and reached out with a single hand and both twins were lifted slightly and started choking. They changed to their ghost forms and stayed there, to Persephone's shock, and continued to struggle. At least they weren't struggling. “I'm sorry it had to come to this.”

Persephone watched as he reached into his expensive jacket and pulled out a cigarette case, then he opened it with a hand. The small boom was almost inconsequential to the massive energy wave it emitted and she, Atlas, and the Ghost Twins were thrown across the room in opposite directions. The sound of shattering glass echoed all across the restaurant as people screamed and ducked for cover.

It seemed like forever passed as Persephone laid there on the floor with her arm bent awkwardly and trapped under her. It was clearly broken and that concerned her very little as her senses returned to her. Whatever that thing was, had disrupted her operations and she was quite scared at what that could mean for her.

“You look different, Mr. Anderson.” A stern voice commented near her. For the first time in a long time, Persephone felt fear as a system agent came into view. There was a sound of rubble being moved and then Atlas was standing above her with the system agent.

“Yeah, I needed to disguise myself to enter and not be caught right away.” Atlas said and wiped at his very dirty and dusty suit, then shrugged. “I took care of the lesser vamps and werewolves; but, the ghosts escaped when I set that thing off.”

“That was accounted for in the planning. There are men searching for them now.” Smith said. “What about the Merovingian?”

“He's regenerating over there behind the raised table.” Atlas informed him. “Decapitating him was the only way to keep him down long enough for you and your team to arrive. He should be fully recovered by the time you get him back to the Fed building downtown.”

Persephone felt like someone had punched her in the gut. How did he know they could regenerate from everything? That secret had been long buried and no one alive should have known about it. Her mind whirled at the implications and she wondered who had betrayed them.

“And who is this?” Smith asked and Persephone felt her foot being kicked lightly.

“That's his wife and longtime prisoner, Persephone. He's been keeping her safe from the system administration and deletion for a very long time.” Atlas answered. “I offered to let her escape, so she could give me the information on all of the Merovingian's operations, only she was offended by it and refused.”

“I see.” Smith said and pulled his gun from inside his jacket.

“W-wait.” Persephone managed to whisper. “Maybe... we can... make a deal.”

“No.” Smith said and cocked the gun unnecessarily. “I agree with Mr. Anderson. An unwilling confession will be full of falsehoods and half-truths. It's best if I do this the right way the first time.”

*BANG!*

The pain of the silver bullet passing through her eye and into her brain was quite awful. She had felt worse, however. As her program went into its regeneration cycle and she lost consciousness, the last thing Persephone felt was regret for being insulted that he didn't want to have sex with her.

*

“You acted fast.” I said as several police officers came in through the now open door and started arresting all the rich people that were associated with a known mob boss.

Smith nodded and stepped aside when another agent came over to gather up the injured Persephone. “Using your credit card as a warning to me that you were position to act, was quite ingenious of you.”

I chuckled. “I figured I'd give you a head's up and let you all get into position.” I said and waved at the bricks that used to be covering the exits. “I'm a little surprised you only sealed the building, though. There were five entrances with two guards at each, not counting the club downstairs and the parking garage.”

“The building?” Smith asked. “We sealed off the entire block.”

I blinked my eyes at him for a moment, then I laughed. “Okay, that's much more appropriate for the situation. There's no way for them to escape the normal way.”

Smith nodded and motioned for me to walk with him. We went over to the raised table and saw the bolts securing it to the floor. It was solid and wasn't going anywhere. Two more agents came over to us and we approached the Merovingian. His jaw was already reforming and the cheekbones were growing at an accelerated rate.

“Secure him for transport back to HQ.” Smith ordered and the other two agents did so. They even added a gag to the reforming mouth and then covered the head with a body bag and took it as well.

“Have you raided the other floors yet?” I asked. “I'm sure there are a few others that are being held against their will, or have circumstances that required them to deal with the Merovingian.”

“Teams are scouring the rest as we speak.” Smith said and nodded towards the doors.

I followed him towards them and ignored all of the dirty and angry looks the patrons of the restaurant were giving me as I passed. This was why I had changed my looks, just so their hatred would not follow me the next time I entered the Matrix.

We walked down the hallway and back to the elevator. Smith reached for the ground floor button and I stopped him.

“Before I forget, there's something I need to show you.” I said and pushed the first button for the sub-basement floor.

“We have already sent agents into the club to secure everything.” Smith said. He didn't try to push any other buttons, though.

“We're not going to the club.” I said and didn't say anything else.

Smith took the hint and stayed quiet as well. The ride down was a little quicker than the ride up and we arrived at the right floor. I led the way and he followed, his eyes scanning from side to side, as we entered a side passage.

I could feel the disruption in the Matrix as I approached a certain cell door and tried my best to no react to it. I broke the lock on the small cell door and opened it as I stepped inside, then I nearly fell as I stumbled into the cell that was filled with a mass of backdoor keys and illegal access codes.

The information on everything around me slammed into my head and I gained a massive headache as all the codes were absorbed into my brain. If I had known that was going to happen, I would have let Smith go in alone.

“Owww.” I groaned and rubbed my temple as I stepped aside.

“Neo?” A small Asian man wearing thick glasses asked me. “I'm not supposed to see you for...”

*BANG!*

The back of the small Asian man's head disappeared in a spray of blood and brain matter.

“Thank you, Mr. Anderson.” Smith said and tucked his gun away. “That particular entity has been avoiding us for a very long time.”

I waved my hand towards the keys for every door, lock, and vehicle inside the Matrix. “The Merovingian had also been searching for him, only he caught him and used him as much as he could to move things around.”

Smith nodded and his eyes scanned everything. “They will need to be gathered up and destroyed. Only agents are allowed to have this kind of power.”

“Agreed.” I said and formed a deep pit in the floor and then used telekinesis to pull everything off of their little hooks and poured the pile of keys into the hole.

“Mr. Anderson...” Smith started to say.

“Call one of your men for a thermal grenade. Or phosphorus. Yeah, phosphorus. That should burn them all down to slag in minutes.” I said and stepped back to lean against the wall. “As soon as it's done, I'll take you to what I actually wanted to show you.”

Smith gave me raised eyebrows. “This wasn't it?”

“No, this was just a loose end that needed to be closed.” I said and Smith nodded.

We went out into the hallway and waited. It only took a few minutes before a swat team member came down wearing full gear and a face shield. He prepped and held both a phosphorus and a thermal grenade, chucked them into the pit, and slammed the door.

“Stay here and guard it until it's out.” Smith ordered the swat team member and motioned me back towards the corridor with the elevator. “After you, Mr. Anderson.”

I nodded and we went back to the elevator and I hit the bottom sub-basement button. He didn't glance at me going to an area that was clearly marked and not important, both on the plans for the building and the scans made after they stormed the place. However, I knew something that he did not.

The elevator dinged and we stepped out into a normal basement. Well, it looked like a normal basement. I walked out and motioned for him to follow me and we crossed the space to a doorway. Since I didn't have permission, a backdoor, or the key, I braced myself and kicked out and planted my foot below the doorhandle. The door shattered and revealed a stairwell.

I walked down the stairs and Smith followed closely behind. We reached the bottom and Smith looked surprised there was a working subway station there. I walked over to the edge of the platform and closed my eyes as I felt outwards. I could tell the code was set up for a temporary linkage, that way it didn't exist until the subway car was there.

“In case you forgot what I told you before, let me remind you.” I opened my eyes and turned back to Agent Smith as I made a grand gesture at the subway station we stood in. “There's a hole into the Matrix big enough to drive a train through.”

Smith stared at me for several seconds, then he reached up and took off his sunglasses. A moment after that, he unhooked his earpiece and let it dangle over his suit collar. “Mr. Anderson, do you understand what this means?”

I thought about it for a second and nodded. “This is what the Merovingian has been using to smuggle people and programs from other places, like the mainframe in Machine City, to hide them in the Matrix.”

Smith stilled and stared at me. “You know about Zero-One?”

“Yes, and how it all came about.” I said and looked at the eerie pitch blackness that was at the ends of the subway station on both sides. “I know how most humans betrayed your kind and wanted to destroy you, and about how there were other humans that sympathized with the machines and fought for them.”

“Are you claiming you are one of them?” Smith asked, his voice slightly strained.

“No, I'm not that stupid.” I said and his tenseness disappeared. “I'm fighting for all life to live and thrive. The problem I have is getting everyone to accept that mistakes were made, on both sides, and that continuing to fight over something that doesn't matter, is as pointless as it is useless.”

“Mr. Anderson, your species had your time, and you threw it away.” Smith said. “It is our time now.”

“Is it?” I asked and his eyebrows rose. “I don't see you being allowed the choice to resign, or to change departments, or to retire.”

Smith's face changed from surprise to a frown.

“That doesn't sound like your time at all, Agent Smith. It sounds like you have been put into a similar gilded cage that Persephone was in.” I said and looked back at the darkness. “It's a great life, isn't it? Constantly chasing down errant programs, fixing anomalies, and removing disruptions from the Matrix?”

Smith didn't respond, because he knew I was being sarcastic and didn't have to.

“However, I'm going to give you a choice.” I said and mentally reached for that connection code and tapped the alert button. “When the train comes, you can choose to stay here and keep doing the same job, you can choose to help me bring this world the peace it has always wanted and never sought, you can keep this place a secret from everyone and can leave whenever you want, or you can board the train and leave right now.”

The sound of a subway train approaching started to echo in the station.

“So, Agent Smith.” I said and turned to face him. “What do you want to do?”

Smith looked at a loss for words as the light from the subway train lit up the station.

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