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Melchior, the Guru of Life, was the designer and architect of the Mammon Machine. Seeing the power Lavos was exerting beneath the earth, it was decided that that power could be used to achieve immortality. When it was completed, it was placed in Zeal Palace. Melchior gave Schala, the princess of Zeal, a Pendant that was capable of controlling the machine. For security reasons, doors were placed around the Mammon Machine that could only be opened with power taken from the machine.
In the original timeline, Queen Zeal wanted the machine activated when it was completed. The three Gurus warned of dimensional vortexes, power beyond human control, and that they will be dragged into a rift if it was activated, though they still proceeded. When it was activated, Queen Zeal, the three Gurus, and Schala were there to witness it. However, Janus entered the room as well, and suddenly they all appeared in front of Lavos. Gates then appear and transport the three Gurus and Janus to different times.
When Crono's party arrives in the Antiquity, they enter the room containing the Mammon Machine in Zeal Palace and hold the pendant to the machine, resulting in it powering up. They use the powered-up pendant on another door and find the Queen, Dalton, Schala, and The Prophet. The Prophet tells the Queen that Crono's party are the "bringers of disaster" he warned her of, so Dalton sends a Golem at them. If they beat it, then Dalton places a barrier around them and the Queen tells them that they will not die yet. If they lose to the Golem, the Queen says the same thing.
The party is imprisoned where the Mammon Machine was previously located. Schala and Janus arrive soon, and Schala releases them, asking that they save Melchior from the Mountain of Woe, though the Prophet arrives and sends them back to the Prehistory The party eventually returns to the Antiquity thanks to the Epoch. They head to the Terra Cave and eventually make their way to the top of the Mountain of Woe. They defeat Giga Gaia and free Melchior from a barrier that was placed around him. They tell him the situation, and he tells them that it "seems the more energy the Mammon Machine absorbs, the further the Queen descends into madness" and that "Lavos is overtaking her soul from within his slumber beneath the waves". The mountain suddenly begins to collapse due to the seal being broken by freeing Melchior, so they flee from the mountain as it collapses into the ocean.
They assemble at a village with the Earthbound Ones. Melchior says that "Lavos sleeps deep underground, consuming the energy" of the planet and that if the Mammon Machine is brought any closer to him, he could awake. Schala and Janus then enter the village. Schala tells Melchior that the Ocean Palace is now complete, where the Mammon Machine was moved to, though she insists that she will not activate it. Dalton then enters the village and forces her and Janus to the Ocean Palace. Melchior says that Schala must be saved, because if the Queen's plans are achieved, then there will be no hope for life. Before they go to stop the Queen from activating the machine, Melchior gives the party the Ruby Knife, which he says is made from the same red stone as the Mammon Machine and that with it, they will be able to destroy the machine.
They head to Zeal Palace and find Dalton. They fight and defeat him, and he enters a Gate, which the party enters as well. They then arrive in the Ocean Palace. As the party goes through the palace, the Queen tells Schala to raise the output of the Mammon Machine to its limit. Schala obeys, and the Queen comments that she feels eternal life flowing into her, though Schala feels "dark energy" and falls to her knees. One of the Enlightened Ones comments that it is too dangerous to continue with the Mammon Machine, though the Queen tells Schala to keep powering the machine as immortality will soon be theirs.
Crono's party eventually arrive where the Mammon Machine is. However, the energy from the machine is too great for Schala and injures her. The Queen tells her to control the machine, though Crono throws the Ruby Knife into the machine. However, the Prophet comments that it is too late, and suddenly they appear in front of Lavos. The remains of the Mammon Machine would appear at the end of the Black Omen where it serves as a boss.