Many numerous theories for the nature of the Monster have been proposed, most offering either a materialistic explanation for it as a purely natural phenomenon, while others have offer primarily supernatural speculations. My central premise is that, just as with humans, the Monster possesses a body/soul dichotomy. Thus, both scientific and spiritual explanations contribute to a comprehensive understanding of the creature.
For clarity’s sake, I will hereafter refer to the spirit/soul of the Monster as “Cerberus,” and the body of the Monster as the “Black Smoke.”
Cerberus is most clearly understood when viewed in similar light to that of the Angel of Death who carried out the slaughter of the firstborn as the final plague against Egypt in the book of Exodus, with Jacob serving a similar role to that of God (though this is not to say Jacob is omnipotent or omniscient, though he is the most powerful entity on the Island, and acts in its best interest). Thus, while Cerberus is a malevolent spirit (though not outright demonic), it is nevertheless subject to Jacob’s authority, and made to carry out his judgments. It is also at times subject to Jacob’s servants, such as Ben, and required to protect them. At other times Jacob holds its chain, denying it victims, as with God and the Accuser in the book of Job.
The Black Smoke itself is more than merely a body for Cerberus. Similar to the Wheel, it derives several of its properties from some element of “fringe” science, (such as exotic matter). Furthermore, the analogy of a body may not be fully accurate, as Cerberus and the Black Smoke were at one time independent entities. Only Cerberus was sentient, and only the Black Smoke was intended as part of the Temple’s security system (confusing the two natures of the Monster, Radzinsky dubbed the underground tunnels “Cerberus Vents”). It was Jacob who imprisoned Cerberus within the Black Smoke, unnaturally bonding it to the material world to limit it freedom of movement as a form of punishment on the spirit for a yet unspecified transgression.
In their final confrontation with the Monster at the end of the series, the survivors will manage to render the Black Smoke inert, unintentionally releasing Cerberus before defeating it once and for all.