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The battle with Perfect Chaos is mostly similar to the original battle in Sonic Adventure. However, without access to all seven Chaos Emeralds, Sonic must Boost to avoid falling into the water and to inflict damage on Chaos. In this boss battle, there are several Star Posts that allow the player to return to specific points of the battle should they die.
For the most part, the battle is a reprise from the final battle of Sonic Adventure. Sonic must travel through the flooded ruins of Station Square towards Perfect Chaos in both 2-D and 3-D perspectives whilst avoiding Perfect Chaos' attacks, which include energy missiles, giant whirlpools and water tentacles. The battle is split up into four phases. In the first and third phases, Sonic must boost into Perfect Chaos to move up his watery body to attack his core. Unlike in Sonic Adventure, it does not matter what speed Sonic enters Perfect Chaos' body with. In the second phase, Sonic must traverse up the rubble of a building and use springs to attack Perfect Chaos' brain with a Homing Attack.
Once Perfect Chaos has been hit three times, Perfect Chaos Revival starts like in Sonic Adventure for the fourth phase of the battle, but the battle style changes as Perfect Chaos causes several platforms to rise up from the watery area. Sonic must then jump across these platforms toward the nearest platform to Perfect Chaos on the player's right hand, whilst still avoiding Perfect Chaos' attacks and falling off the stage, to hit Perfect Chaos' brain with another Homing Attack and thereby defeat Perfect Chaos.
The Hard Mode battle is much the same, but Chaos' attacks are more frequent, and another section is added to the battle before the original fourth section. Additionally, the section where the player is launched into Perfect Chaos' brain is skipped immediately to the third section of the regular mode.
Perfect Chaos is also the only major boss from the past that doesn't appear in one of Eggman's structures.
The main difference with the two fights is that in Sonic Adventure you needed to be Super Sonic to travel across water, but since the release of Sonic Unleashed, Sonic has been able to do this with the Boost so he didn't need to be Super in Sonic Generations.
A remix of the music from the original battle "Open Your Heart" by Circuit Freq plays during the stage, as well as a remix of the second phase Perfect Chaos Revival.
Perfect Chaos has his original roar, which other monsters like the Biolizard also received with a pitch change. To the untrained ear, Chaos also seems to have gained a new cry - he will scream with a very sad tone in his voice upon receiving damage. However, this noise was actually in the original Sonic Adventure but was nearly silent under the music and explosion sounds effects of the battle.
It is possible to drown in the Perfect Chaos stage if Sonic stands on top of a debris that will completely submerge him underwater, making this stage one of the few instances of where Sonic can go "underwater" and drown in a 3D perspective. This is more noticeable in the third phase.
One of the only other times Sonic can go underwater and drown in a 3D perspective is in Seaside Hill.
Perfect Chaos looks solid in Sonic Generations while in Sonic Adventure, it was only water.
Perfect Chaos also appears to be more purple than blue, and possesses what looks like a green horn and green teeth. His skin looks like it is made of scales, which gives him an almost reptilian appearance, while that is not the case in Sonic Adventure.
However, it should be noted that Perfect Chaos had this reptilian look in the opening cinematic of Sonic Adventure, making it possible that he was always meant to look this way.
It has been explained that this was what Perfect Chaos was originally meant to look like. However, due to technological restraints, it was not possible at the time.
This is the only boss fight or rival battle in the console version of Sonic Generations to have checkpoints.
In the phases that launch Sonic into the air to home attack Perfect Chaos, if the player misses and falls, it's still possible to land a hit by boosting up his body, just like in the other phases.
If the battle is paused while Perfect Chaos is "exploding", the scene will shift to the area where Sonic would land for the next phase.