- "He's holding one of the pieces of Claves's soul! Everybody, let's go!"
- —Allegretto, prior to the battle with the Annihilator.
The party braves the many dungeon levels of Mysterious Unison and eventually reaches the lowest level. There, they find Annihilator, holding the final Soul Shard needed to resurrect Claves's soul.
The Annihilator is a palette swap of Ruined Body and carries a similar attack set and even some of the exact same attacks. Its normal physical attacks are a headbutt and whacks with its arms with a chance of knockdown. Its most dangerous Special Attack is Blood Sink, which it uses at the end of a turn, damaging and lowering the attack power of everyone at melee range. Another strong move is Crop Top - three strikes on everyone at melee followed by a powerful energy blast. Scorcher is an arc of blue fire from a slight distance. Finally, Provoked is a powerful whack on a single target with a chance of knockdown. When its HP is in critical, it will use Reclaim at the beginning of a turn to place itself in Regenerate status for 49000 HP per turn, though this wears off after a few turns and it cannot use it again.
The Annihilator has some very strong physical moves, but it is extremely slow and its attacks are generally very easily Guarded against or even Counterattacked. Since it has no great distance attacks, one strategy is to use Viola and Beat, forcing it to move around, or just keep attacking only one character at melee range. The battlefield is almost entirely in darkness with only small patches of light on the edges, so if not using distance attackers, then make use of accessories or other equipment for Shining Body status if desired.
Another strategy is two use two melee attackers and then place an infinite range healer at the edges, such as Polka or Serenade. If using Serenade, she can also pull off a lot of damage with Verbum: Expello unless Annihilator is pretty much all the way at the other end of the field. Alternatively, equip Polka with an infinite distance attacking spell as her second Special Attack, though this likely won't be as damaging as Serenade's move.
Compared to the Unison version of Rondo, this boss likely won't feel like much a challenge. It can easily be defeated at whatever levels were used to defeat Rondo, which may well be 60 or less. Bring a Very Odd Chocolate and Sock Incense into the Item Set to decrease its attack and defense and fill the rest with Angel Trumpets and Goddess Bouquets, and perhaps one or two Clover items, or more if not using a healer. If playing the Xbox 360 version, or not playing in Encore Mode on PlayStation 3, bring in any Saint's Mirror items remaining, since this is the toughest boss left in the game. If the player is halfway decent at Guarding/Counterattacking, then this battle will be mostly one of endurance, due to Annihilator's high HP total.
The musical theme for the battle with Annihilator is "Unbalanced," Track 6 on the fourth disc of the game's soundtrack. This is the same theme used for the battle with Ruined Body. (Ruined Body and Waltz in the Playstation 3 release of Eternal Sonata)
- In the PlayStation 3 version of Eternal Sonata, the amount of EXP granted for defeated Annihilator was reduced by over 2/3 and its HP was reduced by just over half. The Great EZI, the boss of the Church of EZI, carries a higher HP total than the Xbox 360 version of Annihilator, but morphs into Bouncing EZI in the darkness, which has about as much HP as PlayStation 3 Annihilator. Both give less EXP than the Xbox 360 version of Annihilator.
- In the Xbox 360 version of Eternal Sonata, his Reclaim places him a Regenerate status that heals for 99200 HP.
- Upon defeating Annihilator and exiting The Shores of Life, the player is rewarded with the final segment in Chopin's life story sequence, "Heroic."