The Caretaker is building some kind of machine made of souls – literally a Deus Ex Machina. It believes it needs Cain to complete the machine, because Cain possess an ability (or abilities) that Emmanual had but the Caretaker now lacks. Unfortunately, Cain’s soul is twisted and blackened (he’s undead) and the Caretaker feels he must be cleansed before his powers can be used to complete the machine.
The first undead were created by human wizards (now known as necromancers) studying Cain’s remains and using that knowledge to craft unnatural monsters. Once a soul becomes undead, there is no known cure. Gaia considered those souls tainted, and cast them into the sun to be cleansed by its fires. The Caretaker has continued this practice, but is searching for an alternative.
Adam McLean believes in the Caretaker’s machine, and is willing to sacrifice himself and others to provide enough souls to finish it. Also, he and the Caretaker are working on a way to rescue the souls trapped on Mercury so that they can be used for the machine as well.
One current idea is that McLean (probably from the Caretaker) has learned of a prophecy relating to threes. Something about three components of a divine power maybe? McLean mistakenly infers this is referring to the three pieces of the Occultem Lapidem, when actually the Occultem Lapidem itself (when all three pieces are brought together) represents only a single piece: the Divine Conjunction (see Lucas’s entry). The other two are Andy’s character Brice Murphy as the Divine Verb and Lucas’s character Noun as the Divine Noun.
There are other threes as well, paralleling the Hindu gods Brahma (the creator), Vishnu (the preserver) and Shiva (the dissolver) – the Destiny Force is the Creation force, and the Destroyer is the dissolver. However, what about the preserver? Maybe the Caretaker seeks to create a Preserver with its machine. (In actuality, the Caretaker itself could be the preserver – after all, Emmanuel is not from this universe, and the idea that he is from the enclosing universe just like the other two are is compelling.)
Another issue is what McLean is doing gathering unique intelligences (the Saturday group). The current theory is that he is searching for someone or something suitable. Maybe a specific intelligence mentioned in prophecy, or perhaps someone who could be a candidate for some role or process. Vadril Korlax was brought in because whatever property McLean is looking for is something that is not possible for him to identify with an untrained eye – he believes that Vadril’s scientific mind with a specialization in the creation of intelligence will be capable of identifying this quality for which he is searching.
In addition, he probably has a separate purpose in mind for Max Cohen, as one of the other two O.L. holders. He also might be worried about Rae Denison being a threat to Earth.
McLean gooed Mercury on purpose, to harvest the souls for the Caretaker’s later use.
Octopi are remnants of ancient humans twisted by Emmanuel’s touch.
Zee is formed from the soul of John Bishop’s golden dragon. It was cast into the sun to be cleansed, but because the dragon was powerfully psionic, the effect was unusual. The cleansed souls of the sun formed into an oversoul, represented by the phoenix. The phoenix somehow cast the soul of the dragon, now cleansed and connected into the oversoul, back to the Caretaker for it to be reborn on Earth. Thus, Zee’s natural psionicism makes sense.
Vadril Korlax is being groomed to create the program to drive the Deus Ex Machina. McLean hopes that the unique intelligences he has assembled will inspire Korlax to resume his research. The Caretaker is incapable of designing the program itself because it lacks the creativity necessary (its Gaian half is more naturally intuitive, but not an engineer).