He might be forced to kill Ai to forcefully reset her whenever she goes out of the script. In the fake city she mentioned in chapter 19 that she was thinking about dropping out of college because her father had health problems and couldn't pay tuition, and mentions that a teacher overheard and said he could waive some of the fees if she worked for him. Even with all that is happening, the fake city is moving towards the event that got her killed, which is probably key in undoing her death permanently.
If old Makoto is indeed the one killing her repeatedly for his plan, that will probably set virtual Makoto against him.
If old Makoto is indeed the one killing her repeatedly for his plan, that will probably set virtual Makoto against him.