The Order

Chapter 1: A Glitch

Author's note: Got the idea for this story after reading two different X reader stories surrounding the matrix and an online quiz surrounding the film. I don't own the movies or the characters in them but made the cover in MS Paint. Hope you guys like the story.

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Jones's POV:

It was supposed to be an other day for me and the other agents. Yet for the past few days since we brought in a new human. I had started to feel something strange. Her name was Miss Teo Broere as my command unit Agent Smith has spoke of when we interrogated her. Smith and Brown were their usual 'selves' yet I began to think for a second that her name was nice. Fitting for a human like herself. I guess that was when the glitch started. I could have reported it. But for some reason I didn't. I'd heard that Agent Smith had broken the rules sometimes. Maybe his ways were becoming imprinted onto me. But I didn't want to get deleted and replaced and just thought that the glitch would go away on it's own. That I would fix myself and go back to being the program I usually am. We were looking for individuals who we all at the agency called red pills who had tried to contact her. But Smith and the rest of us were in a race against time as Morpheus was unplugging humans from the simulation all around us. Even though I was usually the muscle of the group I knew that if we failed to stop them we might be ordered to go back to the source. Be replaced by other agents who could do the job better then us. She'd asked for us to just give her time to think of Smith's offer of a clean slate but I think Smith just scoffed at it. Yet we let her leave. Only ourselves knowing that we could show up in front of her at any moment if she tried to flee or if one of the red pills like her brother tried to contact her and have her unplugged.

We found a crew of red pills and we took over some humans who were still plugged in. Smith ordering me to kill them and as usual I did as I was ordered to. Killing the humans quickly and effectively as I drove their heads into the stone wall repeatedly. My suit getting a little bloody but I minded a little less compared to how Smith is said to be with things. I killed the last red pill in the crew showing that yet again I was the same agent as before. Yet much to our surprise we saw Miss Broere close by. She saw the sight that was in front of her. The evidence of the blood bath being clear on both my hands and my suit. The red pills looking barely human anymore thanks to how I killed them and the sight appeared to make her look quite unwell. "You have one more to get rid of. Get her" Smith ordered. Clearly telling me to kill her next. My mind only guessing that the offer of a fresh start Smith was giving before hand had now expired. Probably thinking that if she wasn't with us then she was against us, even if she wasn't unplugged. I let go of the pile of flesh and bones that once was a human and turned to her. The brunette looking like she was frozen in place from what she was seeing. "This is the part where you run...goodbye, Miss Broere" my command unit said as he turned around to show his back to her. What was happening only now appearing to register in her human mind as she started to run away from me and I started to go after her. As I heard her run I also heard her calling out for someone to help her and that she didn't want to die. Yet I got closer to her by taking over a human that was closer. Not only allowing me to get to my target faster but also get the blood off of my hands and suit.

I got to the corridor she was at and quickly found where she was. Clearly either hiding from me and hoping I would just go past without noticing her. Or if she was a red pill, she would try to attack me and make a break for it afterwards. I shoved my hand through the door before pushing myself through it. The wooden door proving no match for my strength as it was reduced to splinters around me as I went inside. Slowly starting to strangle the life out of her as only a small half strangled whimper escaped her lips. Before I stopped what I was going as the glitch happened again. As I was being touching in some...personal places. The room she was hiding in was barely big enough for the two of us yet I didn't know if it was the small space or the glitch that was stopping me from taking her life. I looked into her eyes and I felt that I didn't want her to be sad. Felt that I didn't want to kill her as my mind started to argue over if I should follow Smith's order or not. My hand was now loose enough around her neck to allow her to breath more easily yet I wondered what she was thinking. Wondering if I was hesitating? Wondering if I was still going to kill her? Until I felt the glitch start to take over more. I began to feel something happen lower down and I glanced downward to see that there appeared to be a tent in my pants. Even if she was a red pill she would probably be surprised to see an agent. Let alone one like myself have this happen with a human. I then heard her say my name and I seemed to lose myself in looking at her beauty again. Slowly moving my hands to her sides before I looked more into her blue eyes. 

I no longer wanted to kill her but knew if Smith or another agent found out that she was still alive and that I had spared her. I would be questioned for sure about my actions. She looked at me confused but also happy before I came up with a plan and told her to stay where she was. The human I just spared only nodded her head and I left her in the small room. I didn't know what was happening to me. I didn't know what I was feeling. Yet I knew I needed to calm myself down as Smith and Brown would find it odd for sure if they saw me right now. I calmed myself down enough before I got back to the courtyard that was still covered in blood from the massacre at my own hands earlier. Smith turning his head and asking me if it was done and I agreed. The three of us going back to the office to do something I found less enjoyable. Paperwork. I waited for the right moment as if I left too late she might have been discovered by another agent. But if I left too early I would also be arousing suspicion with the agency. I returned to where I was before. The courtyard no longer having the bodies there and I felt pleasantly surprised when I saw she was still in the room I left her in. I told her to come with me and she did so silently. I usually don't see the need to talk to humans. Yet part of my mind was wondering why I for the first time showed mercy to one I was ordered to kill. Why I was doing this. yet again what I was feeling and if I should just report it and go back to who I was. When we got to my apartment she was still quiet. Yet she soon asked me just one word. Why. I said nothing as I didn't know what she was asking me. 

"You will stay here for the time being. You will not leave this apartment alone. Wait until I return and do not go up to the offices" I instructed her. She asked what would happen to her if she didn't listen to me to which I just said that she would die. Not being the whole truth. As I would be killed too. But I chose not to tell her that I wasn't human. She is still a blue pill who hasn't seen the truth behind the façade and she doesn't need to know yet. I told her to get some rest and again she just nodded her head before I left to go back to my office. I still wonder why I spared her life. Why this glitch happened to me in the first place instead of another agent like Brown, Smith or anyone else. yet the thing I felt most curious about of all was why I was feeling like wanting to know her more. All as she was possibly wondering if I should be seen as her saviour. Or her captor.