Meaning "dwelling," Shekinah is the female counterpart to YHVH. She represents the divine presence of God. Shekinah literally means "the presence of God on earth or a symbol or manifestation of his presence," which hints her connection to the Great Will.
The Three Wise Men become one as they transform into their true form Shekinah using the fifth Cosmic Egg formed from the six fruits of the Womb of Grief, after Demeter delivers it to them. The masculine voice and forms of the three are replaced by Shekinah's feminine voice and a bust made of four female faces, facing off against the protagonist who stands in their way.
In battle, she harnesses the fruits gathered by Demeter and the protagonist to attack, each fruit having a different ability stolen from the guardians originally holding them. When near death, Shekinah summons Demeter to heal her at the cost of her life, which the Greek goddess reluctantly does while fearing dying herself.
Healed with the death of her servant, Shekinah continues the fight, becoming highly resistant to all forms of damage except Co-op Attacks. Despite this and added attacks, she's eventually forced to erect a barrier as she nears death again. Shekinah meets her end at the protagonist's hands, with the fifth Cosmic Egg obtained afterwards.
Shekinah is heavily implied to be an avatar of the Great Will, as before dying she apologizes to the Great Will for having failed to guide the world.
Her connection to YHVH (and by extension, the Three Wise Men being YHVH) is implied by Shekinah referring to herself as the god of law, along with the Three Wise Men mentioning that Mem Aleph stole the source of their power and divided into pieces (the fifth cosmic egg/cosmic fruit), which is similar to the EX mission False God in Chains that say that YHVH's power was torn into pieces and sealed away by the mothers of the Schwarzwelt, which implies that Shekinah is in fact YHVH appearing in Strange Journey. Also, before engaging the protagonist, she calls herself Root Shekinah (Shinrei in Japanese, meaning “godly”), further cementing this.
Despite her manipulations, egocentrism and arrogance, she still believes wholeheartedly that her actions are for the Great Will. While dying, she sadly mourns that humanity will slay everything, including the Earth she loves.
Shekinah's initial moveset bears some resemblance to that of Mem Aleph's, packing very strong elemental skills that hit the whole party. Divine Pain is a parallel to Antichthon, inflicting Almighty damage and applying an all-round debuff, and Divine Light is a very strong Expel-based instant kill attack. Fortunately, Shekinah doesn't have Mem Aleph, MA, or Mother's Kiss, so the risk of instant death to the protagonist is relatively low. However, throughout the fight, Shekinah will invoke the powers of the six Cosmic Fruits at the end of the turn, changing her elemental affinities to match the bosses found in the Womb of Grief, and gaining some of their powers to boot. Divine Glare instead reverts Shekinah to her base affinities and abilities.
Once Shekinah falls to low health (20% or lower), she summons Demeter and commands her sacrifice, invoking Eleusinian Harvest which fully restores Shekinah's HP and grants her great resistance to all forms of damage, including Almighty, but excluding Co-Op Attack damage.
Shekinah almost always opens this phase with Heaven's Arrow, a strong gun attack that strikes the party 3 to 8 times, with power rivaling that of Mother's Kiss. She also does this the turn after she reverts to her base resistances. After which, once she starts channeling the Fruits, she begins using the field effects of the bosses, including Cocytus to protect her weakness, Sol Canus to negate buffs and debuffs, and Abyssal Prison to inflict Fear on the party. However, these field effects also end if she invokes a different Fruit or uses Divine Glare. She also gains access to Preening, which not only heals her for over 1000 HP - at this point an equivalent to one or two good Co-Op attacks - but also buffs her an equivalent of four Luster Candies, easily erasing any debuffs you've placed on her and almost necessitating an immediate Dekaja Stone.
While Shekinah is at her base form, not only does she have no weaknesses, thus requiring the player to rely on criticals for Co-Op attacks, but she can erect one of three Toras, which grant her guaranteed reflection from all attacks of party members from any one alignment. The Toras last a good seven turns and persist through different Fruits, but the sole solace is that she doesn't reflect Almighty attacks with them. She does this each time her health falls by around 30%, and the Tora she chooses is dependent on the dominant alignment in the player's active party.
Because this second phase is so dependent on Demon Co-Op attacks, it helps to use demons of matching alignments as much as possible so that you can get quick damage on her. Those that have a variety of offensive elements will serve excellently when she switches her resistances - even the quad-dyne Seth gained from Thoth's EX missions comes in handy. Don't forget that the elemental attack items are still viable when the protagonist lacks the proper element in his gun. When she throws her Toras up, go on the defensive as even Almighty attacks do pitiful damage to her, or switch your demons out for those of other alignments to bypass the Tora. Even the Toras cannot block Co-Op attack damage from the protagonist augmented with Co-Op Enhance W.
"You've done quite well, reaching here... We have bore witness to the full extent of your long journey. You have learned the truth about the Schwarzwelt, and slain the being at heart of it––Mem Aleph. What more could you possibly want, (player name)? If it's mercy you desire, allow us to grant it. You have regained the Cosmic Egg, source of our power, from the vile Mem Aleph. So long as You do no disrupt the god of law's creation, we shall let you be. If, however, you foolishly decide to dabble in the creation of your own world... Your arrogance will be met with punishment We..."
—As the Three Wise Men, just before transforming, New Neutral route
"I, Root Shekinah, shall cleanse your arrogance with divine punishment. The ancient gods and the humans who worship them are no longer needed... The earth is mine alone! I am your god! Your will is of no consequence, Human. You will embrace my mercy. I no longer have need of that song... Now that my power's returned, I shall create a new world myself. Rejoice, for it begins with your death! Your soul will serve as the new world's foundation! Praise my name and rejoice! Behold the rightful ruler of this planet–Root Shekinah!"
—Shekinah, just after transforming, before engaging the protagonist in the New Neutral route
"Ahhh... I am defeated... Reduced to nothing... How frightening... First Mem Aleph, and now you have slain me as well... Man slaughters all... Demons, gods... And even... Earth... O Great Will... It all ends... Woe unto me... I failed to guide... the world..."