both of those are parts of the main story, with the eclysia pyramid part coming first (a lot of the main cast was there, including aelita), and the part with doctor isha coming after. isha also had taken lavender, not venam (since venam was still stone at this point).i agree that itd probably be a good idea to replay the game (or even just revert back to a save file before you started v12) since v13 is coming up