So I'm guessing what happened is that in the original timeline, Miri (Little sister) went to America to test whatever machine they had, and she died. Not just disappeared died. She only disappeared that one chapter because what we see in the manga is Ritsu running a supercomputer simulation. Anyways she dies and he goes on to make the quantum supercomputer in order to find the 'route' where Miri wouldn't die. Trying stuff like prodding her jealousy to get her to stay, but Miri herself always wants to do the experiment (seen by her faking the father's letter saying Ritsu must follow) probably because of some reason related to wanting to be with Ritsu. Fumiko is the supercomputer probably built using Miri's personality.
