"You still will not fall? You are truly the embodiment of filth. Nonetheless... just as darkness is pierced by light, your defeat is part of the natural order of things. Now learn of the humans' filth and its powerlessness before my light!"
The throne chariot of God. It is a four wheel vehicle driven by the chayot which are living creatures with four wings and four faces. According to Ezekiel it is a chariot made of many angels driven by the "likeness of man." Merkabah is made of many Ophanim, Seraphim and Chayots.
"I am the Lord's chariot...the seraph Merkabah. Foolish ones who churlishly the hand of salvation that the lord has extended to you...I shall reduce you to ash for the sake of a new millennium of order."
—Merkabah in first form during confrontation in Neutral Route
After the events of the Monochrome Forest in the Law Path, Jonathan and Flynn awaken at the new Cocoon of Shene Duque and are greeted by the Four Archangels, who call the place the new Mikado Castle. They are informed of Lucifer's return and of how the Yamato Perpetual Reactor has been turned on, releasing hordes of demons upon Tokyo, who would seek to break free through the Eastern Kingdom of Mikado.
Unwilling to allow this, the four have sealed Naraku; but they lack the power to strike against Lucifer. To reach the necessary power to do so, they ask one of the two prentices to fuse with them to summon the Chariot of God, Merkabah, a being powerful enough to fight Lucifer himself. Though Jonathan is horrified at the archangels' plans of annihilating Tokyo and at the fact that whoever enters the fusion will be killed in all but name, the prospect of ensuring Mikado's safety and stability for all eternity is enough to convince him to enter martyrdom by sacrificing himself to Uriel, Raphael, Gabriel and Michael, summoning Merkabah.
In the Law route Flynn and Merkabah defeat Lucifer, as well as Isabeau, and in order to prevent further corruption of the people of Mikado. After that, Merkabah overloads the reactor to destroy Tokyo with a black hole, killing both himself and Flynn in the process to purge their own taint. In the Chaos route, Flynn and Lucifer defeat Merkabah in order to overthrow the Millennium Kingdom. In the Neutral route, it is revealed Merkabah is created from the Great Spirit of Goodwill which is being used by the angels to blindly preserve. Flynn and Isabeau team up kill Merkabah to retrieve the Great Spirit of Goodwill in order to reawaken Masakado to his full form.
"Sometimes called the "heavenly chariot" or the "throne of God." Described as having four faces and four wings in Ezekiel. There is also a form of meditation that invokes Merkabah used to connect to a higher realm. The ritual is quite dangerous, so caution is advised"
—Shin Megami Tensei IV Apocalypse compendium
Jonathan had agreed to enter martyrdom, and fused with the Archangels, leading to Merkabah descending down into the world, and began the war against Lucifer. Their conflict reaches even Tokyo. This later changes with the appearance of Krishna, the leader of the Divine Powers. Krishna claims that he is here to save humanity, in exchange for them offering their souls. Merkabah and Lucifer rebuke him by saying that humanity is their property, and reluctantly form an alliance to deal with the group of polytheistic gods.
It is eventually revealed that Merkabah, along with Lucifer, are actually two halves of the being known as Satan. Created for the purpose of serving YHVH, Satan split its essence into two beings for the purpose of starting a pointless war in order to keep its creator in power. However, Satan grew to doubt God, and upon learning that the Great Will created Nanashi and Flynn as saviors, he decides to test them in combat. In the Anarchy Ending, Satan helps the two kill YHVH, despite knowing it would mean his end. In the Peace Ending, Satan restores life to Jonathan and Walter, long enough for them to defeat YHVH.