In a world where everyone has magic abilities granted to them by Prisms, the continent of Auria declared independence from Tren, which the latter nation didn't take kindly to. In response, Tren developed magic war machines such as cannon-like Derrangers and mobile "Dome" fortresses in an attempt to reclaim Auria, though Auria's Blaze Army has them at a stalemate. Unfortunately, something goes horribly wrong in the war that causes the post-apocalyptic Death World shown in the prologue, where the protagonist, Xero, and his companions struggle to survive against remnants of both armies fighting over resources.
The game then cuts to long before that terrible event, where Xero and his childhood friend, Enda, are playing at their favorite hilltop known as "The Spot." Their peaceful life in the humble town of Ellea is cut short when an omnicidal Tren general, Barclyss, fires Derrangers at the town and wipes it off the map. The two are saved by a Blaze corporal, Slash, and thus begins their journey to survive this war, stop Barclyss's wanton mass murder, and find a new home.
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This game contains examples of:
- A Taste of Power: The prologue has the party at endgame levels due to it taking place in a Bad Future.
- Action Commands: Prism Link skills require the player to input a series of keys or buttons in a limited amount of time. Failure to do so results in the skill being canceled, though only 25 TP will be consumed instead of 100. The inputs become more difficult as players upgrade the Prism Links from the skill learning menu.
- Action Prologue: The prologue starts the player with a high-leveled party that is almost immediately thrown into several battles with soldiers-turned-bandits, ending with the main character in despair over the post-apocalyptic world. Afterwards, the game jumps back to the present and properly introduces the characters and setting.
- Apocalypse Anarchy: The prologue shows that the surviving population of the world becoming lawless marauders who fight each other for resources in a world doomed to famine by endless dust clouds. To bring it home, the boss of the prologue is Sarge, who is normally an ally in the main story.
- Artstyle Dissonance: This game uses Kaduki and traditional RTP-style sprites and some of the monsters are oddly cute. The story itself is still an example of War Is Hell and the game doesn't shy away from using blood or showing suicide.
- Authority Equals Asskicking: The politically powerful people tend to be really powerful fighters as well. Refreshingly this is acknowledged in game, with Heyama emperor's guards saying that they're really just there for show because the emperor could flatten most any attackers by himself. The same is true of a few other characters as well.
- Bad Future: In every timeline except the current one, all of Xero's allies, including Garin, are killed in the post-apocalyptic wasteland and right before he's about to get killed, he unconsciously activates his time magic to send himself back to the point in time where he's at his happiest.
- Bittersweet Ending: The world is restored from its destruction and most of Barclyss's victims are revived. Barclyss himself is given amnesia and stripped of his connection to the Abyss Prism to ensure he doesn't turn into a psychopath again. However, this required Xero and Enda to go back in time, turn themselves into trees, and sacrifice themselves after they wait long enough to reach the present. Slash also chooses to refuse his resurrection in order to reunite with Minake in the afterlife. That said, it's implied Xero and Enda are Together in Death in a more positive form than usual, with the implication that though the visions shown as they turn to trees never happen, the two still live through them. Also, left on the trees at The Spot are two last leaves, which could either imply they're still alive as the trees (even if just barely), or could reincarnate themselves someday.
- Combatant Cooldown System: This game uses its own ATB system via Stamina bars. Unlike most implementations of this feature, the shift key can be pressed to fill everyone's Stamina without taking action.
- Difficult, but Awesome: Each time a Prism Link is upgraded, their damage and effects get stronger, but their input sequence also becomes more complicated.
- Difficulty Levels: Surprisingly, the difficulty setting affects both in-battle factors (damage, Prism Link input time limits, post-battle recovery) as well as puzzle difficulty.
- Doomed Hometown: Ellea is this for Xero and Enda while Parelin is this for Kina, courtesy of the Judgment Faction.
- Duel Boss: There are some in the story such as Farrell and Barclyss's third phase, but most of them are in the stadium's Singles Rank, which only allows the player to use one character.
- Endless Winter: The Judgment Faction bombards the planet with explosive Cosmite rocks, causing the atmosphere to be filled with dust. This makes it impossible to restore the destroyed surface's vegetation, spelling the eventual doom of all life on the planet.
- Everyone Has Standards: The original resistance against Tren kicked out Barclyss when he killed two Tren soldiers that they were trying to non-lethally deal with.
- He Who Fights Monsters: Blaze's Staff Sergeant Higgs suggests destroying a Tren civilian town to avenge Auria's towns. Fortunately, nothing comes of this suggestion.
- Heel–Face Turn: After the Tren brass becomes more aware of Barclyss's goals, they agree to make peace with Auria and help them defeat the Judgment faction.
- How We Got Here: Subverted. The prologue starts the player with an endgame leveled party on a slowly dying planet, and then shifts back to when Xero was a level 1 novice, making it seem like the main story will show the world got to that point. However, Kina ends up attempting suicide and becoming Eidol, which contradicts her appearance in the prologue. Then it turns out that the prologue is actually the previous time loop caused by Xero's time magic. In the ending, the Bad Future shown in the prologue is prevented due to Xero and Enda's sacrifice.
- Justified Save Point: All dungeon save points are powered by the Memory Prism.
- Limit Break: All player characters except Garin have a 100 TP skill known as a Prism Link.
- Magikarp Power: Due to the ATB system and the low cap for AGI, slower characters like Asera and Slash end up being harder to use at low levels, but easier to use at New Game Plus levels when their AGI catches up with the rest of the party.
- Metal Slime: The Apex and Apextu enemies run away quickly and are hard to damage, but killing them results in lots of EXP and PP respectively.
- MockGuffin: The Union Stone does absolutely nothing when combined with the Past Stone and Future Stone, despite the rumors that it can fix a mistake in the past. The intended effect has nothing to do with the stones and can only be achieved by those with a strong connection to the Aeon Prism. This is shown when Xero sends himself and Enda to the past despite lacking the Union Stone.
- Neutral No Longer: After the Judgment Faction attacks Heyama and destroys a large housing complex, the latter nation drops its isolationist policy and eventually helps Auria and Tren in the raid on Fort Cataclysm.
- Non-Indicative Name: So frequent it is probably deliberate. Xero is pretty strong, Slash uses a warhammer, Throg is a poet (though his side quest reveals that's a stage name he got after accidentally turning a serious play into a comedy), and Burns is an earth magic caster. The only one whose name hints at his personality is Barclyss, whose name contains an anagram of Abyss, the really nasty crystal he has a link to.
- Not What It Looks Like: After defeating the Toilet Ham in the Blaze HQ bathroom, the guard outside will ask you this.Guard: "Why were all eight of you in the bathroom huffing and puffing?"
- Playing with Fire: Almost everyone on the planet has a weak connection to the Inferno Prism, allowing them to cast some form of fire magic, though there are exceptions such as Xero. Some characters have a connection to this prism without mastering Fire 1, such as Sandra and Throg.
- Prophecy Twist: When the Future Stone shows a vision that's blue-tinted, it means the vision shown will never happen. Most people assume this means the person the stone was used on will die soon. When used on Kina, it shows a blue vision of her in Glarefrost, which seems consistent when she commits suicide. However, she eventually rejoins the party as an amnesiac long after the events in Glarefrost. When used on Enda, it shows a blue vision of her and Xero sitting peacefully, which is consistent when both perform a Heroic Sacrifice in the ending.
- Puzzle Boss: Several bosses in the Heyama Stadium's Challenge Rank have gimmicks that force the player to meet certain requirements to win, such as how Sickness can kill anyone who doesn't have a specific status effect with its Cleanse skill.
- Rape, Pillage, and Burn: The Judgment Faction annihilates villages and butchers their inhabitants without provocation.
- Reasonable Authority Figure: The Empire, of all people. The commander realizes that Barclyss is going to kill everybody on the planet, so gives Blaze the exact terms of peace that they asked for... with the stipulation that Blaze help fight Barclyss.
- Renegade Splinter Faction: Downplayed. While the Tren higher-ups are no saints in regards to their stance on Auria, Barclyss's Judgment Faction is considered too murderous for them and it intends to eventually destroy Tren too.
- Scratch Damage: Some enemies can only receive one damage, but compensate for that by having low HP.
- Skill Scores and Perks: Characters can learn and upgrade skills by spending PP earned from battle.
- Socketed Equipment: Weapons and body armor have slots for Shards, which work like Materia in that they can duplicate when maxed with PP. There are also some Shards that can give the wielder a portion of the skillset of other characters
- Stupid Evil: In the Bad Future, the marauders kill all of Xero's party members, despite how some of them are probably smart enough to lead the survivors of humanity and help them last a little longer.
- Superpower Lottery: Several characters have Prism connections to Prisms outside of the standard elements, giving them rare spells.
- Tricked Out Time: The two trees seen at the top of "The Spot" seem to have no purpose, but in their Heroic Sacrifice, Xero and Enda travel back to the past before the trees were ever planted and turn themselves into those trees. This allows them to wait for the present with no deviations to the timeline until they're ready to use Enda's life magic.
- Well-Intentioned Extremist: Some of the members of Teyton's Peace Keepers genuinely believe their gang-like organization is for the good of the town and that their "tax collecting" is justified to fund the protection of the citizens against the stationed Tren soldiers. Their "sheriff", on the other hand, has no good intentions whatsoever and is really just an ambitious bully.
