Story starts in the Acorn Kingdom with the player locked up in a cell. The player has made their way to the castle after the destruction of their village. Showing up with torn clothes, exhausted, and half-mad, he was given shelter for a day before making his case to the court. While in the court the player was accused of lying about their village and possibly being a spy for Robotnik -- not only is the player's village far from any other attacks that they've heard about, investigations of other attacks by black monsters have been met with ambushes and attacks by Robotnik's forces. Queen Sally has granted leniency and sent a scout up to the village to confirm the player's story.
The player is interrupted in their thoughts by a guard that's come to retrieve them. The player is brought back to the court and stood in front of the Queen and Antoine, along with the scout that went to the player's village. The scout that reports that she found an abandoned village in the location where the player said they lived. There were signs of fires and stoves that had been used recently but no signs of blood, struggle, or any black pools of ink like reported by the player. The player presses the scout and gets the scout to admit that the area felt wrong and evil in some way. Antoine interjects and accuses the player of lying again, as well as mocking the scout for falling into superstition.
The player pleads to the Queen, saying that everyone is in danger and they know what they saw. The Queen pushes them for more information and the player talks about something they skimmed over the last time they were here, talking about the evil square eye staring at them from the endless void inside the portals that the monsters were coming out of. The Queen looks unsettled at this, Antoine looks annoyed, and there's worried murmuring in the crowd.
The Queen says that, regardless of the authenticity of what the player says is true, there's nothing the kingdom can do to help. She doesn't believe the player is a spy, but their forces are stretched thin and even if the player's village was destroyed there's nothing to be done now. However, she thinks that the player and someone else in the castle might be able to help each other. She says that if the player is willing to, they can work in the laboratory here. Antoine protests but Sally says she's made her mind and asks Antoine to escort the player down. Antoine begrudgingly agrees. The player follows Antoine to the basement where Tails' lab is located. Antoine and Tails get into a quick spat before Antoine storms off.
Tails and the player talk a bit. Tails is wholly uninterested in the player and thinks he was just sent by Sally to bug him until the player mentions the square eye. Tails asks the player about what they know about the eye and ich and is disappointed the player doesn't have more information. He thinks the player might be pulling a joke on him and demands that the player draws him a picture of the eye. The player draws a picture and Tails is both horrified and excited about finding someone who has the same experience as him.
The player asks Tails if he knows what's going on and Tails says no. That's what he's researching. Tails talks about how a few years ago he, Sonic, Amy, and Knuckles tried stopping Robotnik from opening up a warp portal. They failed, and during that encounter something terrible came through the portal and took Robotnik and almost took Sonic. The player asks where Sonic is now and Tails takes him to the tank room with Sonic's body. He says Sonic has been comatose since that day. Knuckles was shot and killed. When the player asks about Amy, on cue a haunting growling/whimpering noise can be heard from down the hall. Tails says something is wrong with Amy.
In summary, something terrible happened that day three years ago and Tails is the only one who saw it. The city has a shield around it now so nobody is able to get into the city to confirm his story or to stop the rift generator that he swears is still running, letting in the evil eye and ich monsters through. The player asks what they can do about this and Tails talks about finding the remaining chaos emeralds and using them to power a machine to take down the shields and then take out the rift generator once and for all. The player agrees to helping Tails.
He gives the player their first task. There's a small group that will do some patrols near the desert edge of the forest. If the player can take a meter that detects the chaos emeralds and write down the values as they travel then that would help. The player agrees and travels with the group. On their way back they're assaulted by a small group of ich creatures. The player must use their skills to save and defend as many of the group as possible. The player returns with any survivors and gives Tails the data. Tails sends the player out two more times. One time goes without any problems, the third time there's a minor scuffle with some remnants of Robotnik's forces.
Tails says that he's been able to pinpoint the location of one of the chaos emeralds using the data that the player gave him. They set off together to the desert. They search around and find the chaos emerald inside the nest of a giant desert viper. The two work together to recover the chaos emerald and head back to the Acorn Kingdom.
The next day Tails shows the player the rest of the lab. He shows that he has Sonic stored in a tank and talks about what happened on The Opening. He then shows the player Amy's padded cell on the other side of the lab. He tells the player about Amy's condition. Later that night he asks if the player wants to try giving Amy some food. She needs to be spoonfed and she'll spend the entire time trying to fuck you. The player can probe a little and decide whether they want to or not. If they want to they'll do the "feeding amy" event and that event will be available during the free time slot.
The next day Tails TBD
The player has three days to look into this issue before the next chaos emerald is located and they'll be forced to look into that instead. There are five different leads that the player has to work with and they can select one each day. If the player gets enough information they'll learn that the person that cleansed the pools is The Oracle and find out where they live. If the player fails all three days they'll miss out on the Sticks scenes and knowledge about how to fight the ich. At the end of each day the player will get a free time slot. If the player goes through the Sticks scenes they'll now have the option to ask people about their history with Sticks.
On the fourth day Tails will tell the player to forget about those rumors, and that another chaos emerald has been found. This time it's in some temple ruins in the jungle. Tails and the player are joined by Archie for this mission, since Sally likes that they've made progress in finding more chaos emeralds. Tails and the player will rely on Archie at a few key moments while navigating the temple. After they've collected the chaos emerald they're stopped by Violet who announces herself as Seer of the Void and that their meddling will not be tolerated. Followers of the cult, including some ich monsters, launch themselves at the trio and at the supports for the temple. They suicide bomb themselves and try to bring the temple down. While escaping, if the party fails enough rolls, Archie will be trapped and killed.
That night the player wakes up with the horrible feeling that something is wrong. Tails wakes up as well when a hideous cackle can be heard coming from down the hall. They look around the lab and discover that Amy has escaped and is missing. They search for her and find her about to cannibalize a random Mobian. If the player has cured enough of Amy's madness then they can convince her to put the man down. If not, she begins eating the man.
Sally shows up and stabs Amy through the heart, killing her. In the aftermath Sally locks Tails/Player out of the laboratory and, after a public session where she covers for their rapey actions, takes them into her private chambers and freaks out and yells at them. In the middle of their conversation a messenger bursts in and says their largest colony has been attacked and razed. Exasperated, Sally tells Tails and the player to get lost for a week while she figures this out and audits their lab.
Tails and the player take a train to a sunny beach resort. While there they encounter Rouge and Shadow who are on a mission to hunt down Koby the Bandicoot in an effort to avenge Sonic's death and bring justice to someone who was indirectly responsible for The Opening. They invite the pair along and they search the casino for Koby. The player has four days to search for Koby before he's kidnapped by the cult and taken back for breeding. During the search the player will be able to interact with Tails, Rouge, and Shadow multiple times depending on what places they choose to search. Regardless of the result the player will get a chance to spend alone time with the character that they made the best impression on.
Once Tails and the player return they are cleared of any wrongdoing. After doing investigations into the attack, survivors reported that a partially-mechanized rabbit led the attack, putting Bunny Rabbot under suspicion. While investigating her activities they found several suspicious movements of materials and encrypted communication with unknown parties. On the other hand, Tails' insistence on adding more security to the colony (after being threatened by The Black Goat via Amy) saved many lives that day. Additionally, while some of their work's subject matter is odd and concerning, there's no denying they're following the tradition of the Emerald Guard by continuing to recover emeralds. Their contributions to the safety of the kingdom is worthy of praise. Bunnie is currently being held in prison and will be executed in three days after a trial for treason.
If Amy survives the doctor comes to get Tails or the player and Tails depending on the player’s actions. He lets them know that somehow Amy’s child has genetic data from both Tails and the player. He will let the player know that Amy already knows that they’re both the father and word has gotten out. Tails and the player go to talk to Amy. On the way out the player will be confronted by whoever they’re dating, if anyone, and that relationship will be over.
The next segment of the game is a Phoenix Wright-style trial and evidence game. Bunnie requests that Tails and the player help prove her innocence. Baron Remi LeQuire, a prominent royal court member, will be the prosecutor. Each day there will be a trial and the player/Tails will have a few actions per day to find evidence to prove Bunnie innocent. In reality, Bunnie was helping Beatrice LeQuire escape and hide from her father, who had raped her since she was a child and continues to do so even as an adult. If the documents that Bunnie hold are decrypted then Beatrice will be exposed and her father will collect her. The suspicious activity related to supplies is her not only skimming some off to sent to Beatrice, but also going against orders from Antoine to move extra supplies from better-off colonies to send to worse-off colonies that she still thinks have potential to help the kingdom.
Multiple endings can happen depending on how the player does during their investigation:
- If found guilty, Bunnie will die from being executed by Antoine
- If found innocent but it's because the papers were decoded or Bunnie was linked to Beatrice, and Beatrice has not been found, Bunnie will murder Remi. She will later be executed
- If found innocent but it's because the papers were decoded or Bunnie was linked to Beatrice, and Beatrice is in the courtroom, Beatrice will kill herself
- If the player can find enough clues to prove the bad character of Remi and the good character of Bunnie, and persuade the judge well enough, Remi will be sentenced to be executed instead
With the trial over, Tails and the player are now on the hunt for the last missing chaos emerald. The next mission continues indefinitely, until the player finds a clue as to where the emerald is. The player gets to select which region of the world they'll search next, which also selects the military unit that they'll travel with. The events that happen in the areas are randomized, and the chaos emerald could be in any three of the areas. As soon as the player discovers a clue, wherever the emerald is, Tails, the player, and Chase will head out to get the emerald.
The trio go through the temple and locate the chaos emerald. On the way out Violet shows up once again with two of her disciples. She feeds them from her breast, writhing and moaning in ecstasy as they drink hungrily the transformative ich from her breasts. Both of them turn into tanks and charge at the trio. They're forced to flee back into the temple and must use environmental objects and traps in the temple to defeat the tanks. Like last time it is possible for the third wheel, Chase this time, to die if the player fails enough rolls. Once they leave they go back to the castle.
While Tails works on putting together the device that can shut down the warp drive Sally assigns a mission to the player. They need to try and find the nest of the cultists and destroy it if possible. Once again the player gets four days to explore, finding clues, and possibly finding one of the lairs. The player will need to go into the lair with a team, slaughter anything inside, and burn it to the ground. If the player fails they will miss out on lore and sex scenes, but nothing critical to the game.
Finally Tails has his device ready. Tails, the player, and multiple other warriors (including Archie and Chase if they're alive) head towards the laboratory with the warp drive. When they get there they find Violet and her followers protecting the drive. If the player has learned spells on their journey they can use them now, sacrificing sanity and power to aid in the battle. The two forces fight while Tails sets the machine up.
As Tails activates the machine Violet cackles and raises her hands. She summons the seventh, lost chaos emerald above her head. Beams of power from Robotnik's machine and Tails' machine converge onto her chaos emeralds. All chaos emeralds break free from their devices and begin to spin around Violet. She rises in the air. She talks about receiving the power of The Black Goat and becoming the ultimate being to rule over this world. She starts shrieking in pain as light emerges from the chaos emeralds and washes over her. Her fur falls out, her skin begins to melt, and her body collapses as she falls apart. In her place stands Sonic, ghostly white, glowing with power, the chaos emeralds circling around him.
Sonic lowers to the ground. Tails rushes to meet him and embraces him. Tails apologizes for failing Sonic and Sonic consoles him. Tails mentions also losing Amy and Sonic glows again and generates Amy a new body, a process that's the reverse of what just happened to Violet. Amy collapses to the ground, confused as to where she is and what happened (although in time she does remember everything leading up to her death).
As this goes on The Black Goat's eye moves ever closer to the portal and tentacles start to pour out of the portal. Tails asks Sonic what he can do and Sonic says nothing, only he's able to solve this. The chaos emeralds begin to vibrate, and after a few moments a tremendous crack is heard as they all shatter at once. Some shards scatter, others fall to the ground lifeless. A horrible moaning roar of anger can be heard as the portal begins to close. Sonic begins to disintegrate, his dust sweeping back into the void. Sonic talks about this being the only way, that if he's the only one the Black Goat takes then it's worth it. Asks Tails to take care of Amy and eat a chili dog for him. Tails tries to follow after him but the player and Amy grab him. Tails screams angrily at the void that this isn't over and he's going to stop The Black Goat and get Sonic back. With a final mocking cackle the void closes and it falls silent.
