If the player is on the Anguished One's route, the Anguished One must be dispatched, and must survive throughout the entire battle. As the Anguished One cannot overthrow Polaris himself (or even damage him, for that matter), a game over is also issued if all other human leaders are defeated.
The fight with Polaris comes in 3 stages. During the first stage, Polaris is effectively immune to everything save Almighty (which he resists), being capable of reflecting Physical attacks and nullifying every elemental attack, in addition to possessing several powerful skills and infinite range. Instead, the player has to weaken him by the defeating the Guardian Stars scattered across the battlefield, gradually reducing his defences, before being able to attack Polaris himself.
Polaris carries a unique skill called "Heaven's Wrath", which deals almighty damage for each Guardian that exists on the field. Therefore, the player must destroy all Guardians in order to minimize the damage. Unfortunately, after several turns, a defeated Guardian will be resurrected. However, Polaris will not recover its skills or resistances that were lost after the defeat of a Guardian.
For the next stage, Polaris gathers all his Guardians to form his full body. What happens depends on the route the player has chosen.
If the player is on the Anguished One's route, the Anguished One is sealed and prevented from taking any actions outside of skirmishes. The player has to attack and defeat Polaris to move on to the next stage, while fending off several strong demon teams that can harm the Anguished One.
If the player is on Yamato's route, the player has to defeat a number of strong demon teams to proceed.
If the player is on Ronaldo's route, fewer demons need to be defeated to proceed. However, Polaris also introduces 2 civilians which can be killed by the demons in one shot, and the players must prevent their deaths. The demons will prioritize on moving towards and killing the civilians.
If the player is on Daichi's route and chose to restore the world, Shadow forms of the Demon Tamers are summoned, mocking the player's choice, and they must be defeated to proceed. If the player has chosen to kill Polaris on that route instead, Polaris decides that their will to fight stems from the protagonist and summons several demon teams to attack the protagonist. Polaris must be attacked and defeated to proceed, but from this point on in the battle, if the protagonist is dead a game over is issued.
For the final stage, Polaris takes on a more bulky form, composed of 3 parts, labelled Polaris A, B, and Ab. Polaris A, the main body, is capable of firing Supernova, a large laser which inflicts Almighty damage to all teams standing in its line of sight. Fortunately, there are 3 conditions to take note regarding Polaris' Supernova:
- Polaris always telegraphs the attack by using Star Compression the turn before.
- Polaris always rests for a turn after firing Supernova.
- Polaris only uses Star Compression if no team is within 3 squares of him, otherwise, he will simply engage that team in combat.
Polaris B, his right shoulder, possesses strong Physical strength along with infinite range, and Polaris Ab, his left shoulder, constantly summons another demon team (via Magnetite Conversion) into the battlefield each time it gets a turn. Only Polaris A needs to be defeated to end the battle, but Polaris B and Ab will increase the difficulty in defeating Polaris A by increasing his offensive and defensive strength respectively. Polaris is also capable of reviving Polaris B and Ab if they are defeated.
If the player is on the Anguished One's route or has chosen to kill Polaris on Daichi's route, Polaris B and Ab have their Racial Skills altered to give all Polaris bodies access to Double Extra and a Beast Eye ability, making both of them a greater threat to whoever gets attacked by any part of Polaris. Barring Supernova and Megidolaon, the largest source of damage coming from Polaris and his companion stars is mostly Physical damage, so prepare teams with Physical resistance (preferably Reflect, since Polaris A has Pierce). As Polaris A has no resistances other than an immunity to Curse, you are free to use whatever attacks you see fit to defeat him.
- Polaris' predecessors (Thuban and Vega) are stars that acted as the pole star in ancient times. Kawkab, however, means planet in Arabic and is very likely a mistranslation of Kochab, an actual previous pole star. Eli is instead a variant on the name of God as spoken in Arabic, Hebrew, and Aramaic; however, it could likely be a mistranslation of the star Errai, which will indeed be the next pole star after Polaris.
- Polaris survives in the Restorer, Meritorious, and Egalitarian endings as the entire fight with him could simply be a means for him to test humanity's resolve. In the Liberator and Kingmaker endings, however, as Polaris' life is at stake, there would be no need for such a pretence. This would also explain why his "binary stars" have abilities that make the fight much more difficult then, as Polaris is using all his power to oppose the party's intentions.
- Polaris, in both Ronaldo's and Yamato's routes says he desires the world to be the way the party wants it to be. For example, he says he also desires a merit-driven society in Yamato's route. This gives Polaris a contradictory point of view, but since he appears in the Meritorious ending scene, it is possible that he really wishes for such a world and had lied to Ronaldo, uncovering a darker side of his spirit, or, from a purely holistic point of view, all he wanted was to test the human spirit and ensure the next step in human evolution was taken, no matter in which direction.
- Polaris' individual parts of his third form are named after its individual component stars since the actual Polaris is a multiple star system. Polaris A is much larger and brighter than Polaris B and Ab, thus it is used to name the main body.
- If the player chooses to kill Polaris in the Liberator ending, he will tell the party that they will no longer be able to wield the power of demons, making him similar to Babel in a way.
- In the game, Polaris only grant the wish of mankind and won't grant a wish of single person alone, which makes the Protagonist must convince as many Demon Tamers he could convinced to join him. However, in the anime, Polaris will grant wish for anyone who survives his judgement even if it's only one person.