Chaos reigns supreme over the ocean, to fight the darkest depths below.
Waves of Change (Four Parts)
To restore their world to normal, the Freedom Fighters set out to find the mysterious Gaia Temples. Sonic, Amy, and Rotor begin searching for one when they are summoned by a young priestess, named Coral the Betta, to her underwater city of Meropis. Unfortunately, it doesn't take long for things to go wrong. The guardian Chao she is tasked with taking care of is strangely dormant, she is under heavy scrutiny by the king and queen, and a mystical barrier protecting them all is on the verge of collapse.
For Sonic, whose biggest weakness is the inability to swim, this is all stressful enough without an evil presence preparing to terrorize the city and its shrine.
Light in the Darkness (Three Parts) & Consequences (Epilogue)
Using a datamined resource file from the Death Egg, Sally sets up a team to find the elusive Chaos Emeralds. They seek out the first one in an abandoned mine, hoping to leave without Eggman noticing they are even there. However, what they also find has Sally make a decision that may make the rest of their quest difficult.
Later, Eggman receives a report from one of his Egg Bosses concerning the Freedom Fighters, and makes plans with another to finally get back at them.
Tropes for Waves of Change:
- Big Damn Hero: Sonic and Rotor return to Meropis to fight off the monster horde. However, when they are on the brink of drowning, thanks to taking a pair of undercharged Air Charms, Chaos arrives to assist and provide a pair of Bubble Shields for them both to breathe in and maneuver.
- The Bus Came Back:
- Queen Angelica complains that they need to worry about Akhlut the Orca's Egg Army along with everything else currently going on. Akhlut was a Grandmaster of the Dark Egg Legion back in the old universe. He would officially return as an Egg Boss in Sonic Universe's "Eggman's Dozen", changed from feral to anthropomorphic like Muttski.
- An epilogue page reveals that Mighty the Armadillo and Ray the Flying Squirrel have been undergoing some training and are ready to make use of what they have. This marks their first time debuting in the new universe.
- Came Back Strong: Contrary to Coral's fears, Guardian Chao Aquarius wasn't dying from the betta's lack of care. She eventually hatches from her egg to become an even stronger Chaos Chao because of her incredible care ever since she had begun her duties as priestess as well as the ones before her. It had just taken longer than expected.
- Cassandra Truth: Sonic explains what has happened at the surface, as well as the rest of the world, to lift some of the burden off of Coral. King Puff deems it too farfetched to believe. Queen Angelica questions how a single person, even if it's Eggman, could possibly shatter the world when the oceans haven't drained away yet.
- Earn Your Happy Ending: While they are unable to find a Gaia Temple, Coral's name is cleared after the guardian Chao Aquarius evolves and helps the heroes drive the Dark Gaia's Minions away from Meriopis. Amy is taught by Coral the sacred "Mystic Melody", which can help the Freedom Fighters search for it more easily. As an added bonus, they are given a cache of Rings to fuel the Sky Patrol.
- From Bad to Worse: As if the planet breaking and Eggman trying to get the Chaos Emeralds and Gaia Temples for himself aren't complicated enough, there are now reports of terrifying shadow creatures attacking all over the world at night as well. It would soon be revealed that these creatures, dubbed "Dark Gaia's Minions" have been formed by the strange energy that is "poisoning" the world and affecting all manner of people, according to Tikal. The energy itself is also interfering with Tikal's spiritual communications near select mystic points, which is why she was unable to defend Coral at the time when she was in trouble.
- Guilt Complex: Coral always feels like she is not worthy enough to carry the title of priestess and worries she may mess up. It doesn't help when she discovers that Aquaris, the guardian Chao, is unable to wake up from her cocoon after performing an evolution ceremony, and the rulers of Meropis blame her for it, among other things. It gets to the point where she believes she is somehow causing the Chao to die. Luckily, the encouragement and assistance from her old and new friends help her restore the fallen barrier protecting Meropis and vanquished the monsters, and the truth behind Aquaris' delayed evolution clears Coral's name.
- Light 'em Up: The Eusebes Shrine exists as a source of light magic for Meropis across the reef. The combined power of Aquarius and a chosen priestess like Coral the Betta are needed to maintain a light-based barrier around the city in order to keep out unwanted forces. With Tikal and Pearly's help, Coral and a Chaos Chao Aquarius use their Mystic Melody to fire beams of light to vaporize the Minions, and at least weaken the stubborn ones for Sonic and the others to finish off.
- Mythology Gag: Once the monsters are defeated, Rotor analyzes that the Meropian waters had been murky ever since Sonic took down Eggman's Egg Carrier a while back. Amy offers to find some way to clean up the mess, but the rulers vow to take care of it themselves as token of thanks.
- The Reveal: As Chaos helps the heroes and people of Meropis, Rotor believes that the creature's power is the reason why the oceans are held together despite the planet being in pieces.
- The Stinger: Elsewhere, a guru-like sloth informs his pupil that his training is making headway, keeping his attitude under control while working on his strength. When asked why he is still "burning" within, the pupil, Mighty, feels like he is ready to make use of what his power.
- Super Not-Drowning Skills: Air Charms are carfted and charged to allow any land dwellers to talk and breathe underwater without the need of gills. However, they deactivate when out of power, which becomes a problem for Rotor and especially Sonic when the latter accidentally takes a pair of undercharged ones. Chaos saves them both from drowning by giving them Bubble Shields.
- This Cannot Be!: Pretty much everyone in Meropis who knows of Aquarius are horrified to learn she is still dormant and assume the worst. She gets better, though.
- Why Did It Have to Be Snakes?: Pearly the Manta Ray is completely creeped out by the Chao residing in Eusebes Shrine. Amy encourages her to face her fear so she can guide the Chao to safety when the monsters attack.
- You Are Worth Hell: No matter how much responsibility or hardship is stacked on Coral, Razor the Shark refuses to leave her side. An origin story reveals that she saved his life after his old gang betrayed him and she nursed him back to health.
- You Have Failed Me: Poor Coral loses her title of Priestess for a while, when Queen Angelica hears of Aquarius' condition and the girl's claim that a "spirit" had told her to bring Sonic's team in. She gets it back after she helps vanquish the monsters, the Chao turns out okay, and they learn everything with Chaos supporting her and the heroes.
Tropes for The Light in the Darkness & Consequences:
- Generation Xerox: On their way out of the mine, Sally's team deals with a strong Badnik resembing E-102 Gamma. According to Tails, Eggman has been mass-producing E-1000s from this specific unit sometime after the destruction of the original Gamma.
- Honor Before Reason: Sally's original plan was to search the abandoned mines while security is down and extract the Chaos Emerald before anyone else notices. They find a cave full of crystals that have no value whatsoever, but is a visual beauty to behold. Sally then decides to adjust her plan to make enough noise to let Eggman know her team was there, all so he ignore the mines after instead of needlessly destroying them for nothing. Nicole protests this deviation at first until she takes a view for herself from outside her handheld.
- Maybe Magic, Maybe Mundane: Tails and Nicole discuss how the Chaos Emeralds keep scattering to random areas after use. Tails believes there may be some magic involved but Nicole, a computer AI, believes there is logic behind the phenomenon.
- No Good Deed Goes Unpunished: By gaining Eggman's attention and leave the crystal mines untouched, he now knows that Sally is using his resource data to find the Chaos Emeralds. He turns to an Egg Boss named Thunderbolt to teach the Freedom Fighters a lesson, by using an Emerald she had just found as bait.
- The Reveal: Sally had snuck into the Death Egg on her own to find valuable data. The files she took turn out to be resource logs that include records of potential Chaos Emerald spots.
- This Cannot Be!: Clove's sister Cassia freaks out a bit after seeing that their dig stie has been ransacked. Clove herself reports what they find to Dr. Eggman, which both suspecting that the may be a leak in information since the co-Egg Bosses were the only one who knew of the Emerald's power reading. This tips Eggman to why Sally infiltrated into the Death Egg on his way back.
