If I can share how I think things may have gone down taking points from GUT and the new info:

-Once he got the resources for it, Marisbilly managed to built and activate Chaldeas for real. In that moment, he took the designer baby he had been raising as his own daughter (Olga Marie) and splitted her soul from her mind/body. Then connected the Soul with Chaldeas so it would function as the Brain of Chaldeas before Chaldeas could generate one naturally on its own. This Soul became Archetype:Chaldeas aka the Alien Priestess. Marisbilly then falsified the compatibility records so Mind/Body Olga would never use rayshift because she going into Chaldeas would cause a bug in the system. The equiptment in Chaldea was probably bugged as well to give a negative in case Olga tried to do the analysis by herself.
(Worlds where he can't activate Chaldeas, Olga is useless to him and he discards her)
-Once he got everything fully operational, Marisbilly remembered Romani's warning about the end of the world (I'm assuming Solomon turned into a human right in front of him and shared his last vision before going world trotting) and use Chaldeas and the other experiments to look into the past and the future, and then discovered Goetia's singularities. He hided the information under a timer so the singularities wouldn't be notice till some years later and started the Crypters project as a way to counter them so they didn't interfer with his plan.
-However, once Lev threw Olga inside Chaldeas, the bug Marisbilly feared started happening. Chaldeas (the system) recognized the new Olga inside of it as its brain as well. Plus the torture Olga was experiencing and her cries for help send signals to Chaldeas that the Brain was in distress which complicated the job of the actual Brain, the Priestess. So in that moment, the Priestess started a plan on how to expel Olga from Chaldeas. At the same time, she needed the singularities resolve, so she summoned and send the Detective, the Professor and the Count to aid Chaldea in solving the Incineration.
-Using all the experiments connected to Chaldeas, the Priestess managed to predict the events of EoR as well (That's how Holmes knew that Shinjuku may exist if the Incineration was averted).
-Then, the Priestess contacted Kirsch under the pretense of the Alien God ploy. She wanted Kirsch to nurture a Fantasy Tree to give Olga a new body with which she could get out of Chaldeas. She also altered Olga's memories so she bought into the fictional story, the fact that Olga's first action once she descended was to obliterate the Lostbelt was probably something the Priestess programed into her mind. I imagine that the creation and manteinance of the Lostbelts and Fantasy Trees costs a lot of energy that Chaldeas needs for something else, that's why getting rid of the Lostbelts helps Marisbilly/Chaldeas plans, because the resources come back to Chaldeas and that energy can be employed in its intended purpose. Kirsch asking for the other members just hindered the Priestess plans even more because instead of one now she needed to make 6 extra Lostbelts.
-Douman then gets summoned to explore pruned worlds to use in the LBs. Kirei and Muramasa get summoned to aid the descent of the Alien God (Getting Olga out of inside Chaldeas) so they collaborated with the Crypters for this purpose. Meanwhile, the previous set of Apostles kept on helping Guda's crew get rid of the extra Lostbelts (and all Lostbelts).
-Now onto Marisbilly's plan, I think he intended to enclosed the entire universe inside either Chaldeas or the planet Earth, then let humanity live on Chaldeas surface, where the Priestess (the brain of the system itself) would guarantee the preservation of Humanity and the Human Order forever as its overseer, correcting any threat or deviation. The universe had to be seal away not only for fuel but because of its uncalculable threats.
-Bluebook's world (Chaldeas simulated world) got bleached as an energy resource, Bluebook himself got sacrificed to kept the ploy of the Alien God going on and place on Traum. The Earth surface got bleached because the Priestess swapped the textures. All signals from the cosmos stopped because the universe is already trapped inside Chaldeas, the galaxies we saw inside the Fantasy Trees are the actual galaxies being used as fuel by the Priestess, once the Fantasy Trees were gone, the galaxies returned to her to use as she pleases. And this is why, (most probably) the Priestess complained on the first Part 2 PV that the universe tendecy to create stuff to fill itself with was its worse trait. This is also why Daybit said this plan would put humanity in the universe shit list but also why the Human Order may opposes now, as basically at this point Guda's crew is threating its own guarantee preservation (the system itself basically got turned on us).
-Beast VII proper is Chaldeas. Olga's Saint Graph gave such a reaction because of her connection to the Priestess and in turn her connection with Chaldeas.