What really happened to virtual Franz? Is he dead?
Franz Hopper is alive and well, is my opinion. He will be a utilized much as Aelita was in Seasons 1 & 2. Whenever uber-X.A.N.A. strikes, the gang will counter the attack with his help. There are several reasons for this: (1) Hopper's greater experience in fighting X.A.N.A. and intimate knowlege of the supercomputer system itself will allow the kids an edge in the struggle. (2) Now that Aelita is fully human once more, she MIGHT now be recognized by the Towers and admitted inside. Ergo, it remains up to Franz, now a complete virtual being, to accomplish the job.
What happened to Aelita's mom? She just disappeared from the flashbacks...
Though the episode definately doesn't say it, I believe Aelita's mother died in some accident when they all lived in the mountains. It an artistic way of removing her from young Aelita's life.
What happened immediately after Franz and Aelita were virtualized? Did The Man ever find the Super Calculator?
We'll appearently find that out once Season 3 or 4 kicks in.
My own question lies in the fact that Hopper kept utilizinf the "Peturn to the Past" protocol (over 1,061 times if I remember correctly) to continue work on Project Carthage. Since we all know that X.A.N.A. grows stronger with every time warp, it remains for us to out WHY X.A.N.A. rebelled and assumed control over the virtual world.