I really enjoyed the story and wanted to imagine its continuation so this is just my brainstorm:
SI wants to prove either:
a) the world narrative exists, free will is an illusion, and the SI can't change anything.
b) the world narrative doesn't exist, free will exists, and the SI matters.
Change 1: When Misaka 00001 and Misaka 00002 connect to each other, Misaka OS 1.2.4 is stored as a backup file on the Misaka Network. After Misaka 00001 dies, her neural mapping and their Meta knowledge is saved to the Misaka OS 1.2.4 file on the Misaka Network but due to the SI's anomalous nature, the OS becomes something akin to a virus that then runs the Misaka OS 1.2.4 on a forked process deep in the background of the Misaka Network.
Accelerator continues on with the Level 6 Shift project but is filled with doubts and uncertainties about whether or not the Sisters are alive. While most of the Sisters are the usual, there are still a few that exhibit strange actions or expressions either in fighting or dying (caused by the Misaka OS Process (MOSP)) that keeps his doubts lingering in the back of his mind.
Note: Toaru wiki states there were 20,000 clones at peak and 9,969+ at end of the original Level 6 Shift project.
Change 2: After hundreds or thousands of experiments, Misaka #X crashes which requires it to restore from a backup. The Misaka OS 1.2.4 Process (MOSP) takes advantage of this opportunity to integrate itself into Misaka Clone #X. This means the Level 6 Shift project is further along than originally and that large numbers of Sisters are already moving around Academy City. This increases the scope of the story to allow the introduction of other characters like Kamijou, Misaka, or others. The Sisters also become a more relevant force beyond just the one-on-ones against Accelerator and not so easily stopped.
From here two storylines could emerge (my favorite is Storylines are 1b with 2a):
Misaka Network Storyline 1
Integration allows MOSP to come to the fore, have greater priority over Misaka Network resources, and starts downloading/integrating itself into more Sisters. It initiates the World Narrative project whose goal is to determine the existence/non-existence of the World Narrative and thus the Sister's status of having free-will or a predetermined fate. Depending on the amount of Meta knowledge it's retained, it's method could be getting Accelerator to kill Touma as originally or MOSP hypothesizes its own method.
a) If MOSP knows at least up to the end of the Level 6 Shift Arc, it's objective is to kill Kamijou Touma for the original SI's reasons.
b) If MOSP has limited Meta knowledge and believes itself to be an integral part of driving the World Narrative, then it will use it's own destruction/non-destruction to determine the World Narrative. Thus, MOSP will fight to take control of and eventually destroy all the Sisters and the Misaka Network. Especially if MOSP has Meta knowledge of the following:
Value of Sisters and Misaka Network.
c) If MOSP has Meta knowledge of Aleister's plan, then it knows that the World Narrative cannot be determined by failing the Level 6 Shift project or destroying all the Sisters. This is because the principles of Aleister's plan will always make project failures pointless in determining the World Narrative as there are backup projects for anything and everything (
Principles of Aleister's Plan). The only solution is to fight Aleister in order to remove him from power. This has a high likelihood of determining the World Narrative as Aleister seems to be its driving force (at least before New Testament). Cue the big brain idea on how to fight the overpowered Aleister who uses UNDER_LINE to monitor everything in Academy City in real-time
Accelerator and Misaka #X Storyline 2
Misaka #X will continue with the Level 6 Shift project but only to buy time for MOSP to gain total control over the Misaka Network. Therefore, there is no need to mind security clearances. Misaka #X will be willing to tell Accelerator about the current situation and what MOSP is currently planning. This portion of the storyline would allow the entry of other characters into the conflict like Railgun or Touma.
a) Misaka #X and MOSP are two separate entities. MOSP's integration process provides Misaka #X with more complete Meta knowledge while MOSP's own Meta knowledge is further corrupted (MOSP losing some Meta knowledge could be evidence for the World Narrative existing and wanting MOSP's failure). Misaka #X knows the Principles of Aleister's Plan and that MOSP's plan (Storyline 1a/1b) will not determine the World Narrative and will seek Accelerator's help to stop MOSP from causing pointless deaths. Accelerator is informed of the World Narrative project and its fallacies and helps Misaka #X. Accelerator recognizes that the Sisters have free will and are people by the very fact that Misaka #X and MOSP are moving beyond the parameters of the Level 6 Shift project. Accelerator will work towards invalidating the Level 6 Shift project.
b) Storyline 1b is used, Misaka #X is a full MOSP clone. MOSP describes to Accelerator the premise of the World Narrative project as follows:
- The World Narrative represents the Sister's programming and the parameters of the Level 6 Shift project.
- The goal is to determine if the Sisters have free will and their fate isn't predetermined.
- Anything short of the complete destruction of the Sisters and Misaka Network won't be conclusive enough to prove free will (Valid since MOSP bases this on Meta knowledge. Even if the Meta knowledge is corrupted, the premise is sound due to the events of Misaka 00001's encounter with Accelerator - None of which a regular Sister could have come up with or planned for. Still invalid when explained to anyone else as you can't really prove to others that your Meta knowledge is real instead of a random but fortunate coding error that lead to the anomalies of the first fight).
MOSP could seek Accelerator's help in exchange for the weakness Misaka 00001 used to bypass his power and the name of Kamijou Touma. Accelerator might help just for that or he'll stop participating altogether as the Sisters are no longer following the parameters of the Level 6 Shift project.
Honestly, I don't a good enough idea for Accelerator possibly helping MOSP. The premise requires belief in Meta knowledge which can't really be proven to anyone other than MOSP. Thus, the World Narrative project has an invalid premise and Accelerator might decide to work against MOSP out of guilt for murdering so many Sisters. If Accelerator helps MOSP, then this sets things up for Accelerator to fight Railgun, Touma, or other.
Factions for all the above:
Accelerator
Railgun & Touma
Sisters
MOSP (name subject to change
)
Level 6 Shift proponents
In order to stop MOSP, the World Narrative project needs to be proven as being fallacious. Either through formulating a different method of determining the World Narrative that MOSP can accept or by fully invalidating MOSP's project premise via "I'll break that illusion of yours". Maybe Touma's fist is capable of making MOSP recognize reality?
Could somehow resurrect original SI to stop MOSP as well?
