In the cutscene before the level, the President of the United Federation receives a call telling him about a data attack on the government mainframe - one perpetrated by Shadow himself if the player has completed Digital Circuit. Shadow teleports from/is teleported onto a large computer-like object where Shadow catches a glimpse of Dr. Eggman. Wondering if the doctor is the right person to interrogate about his origins, Shadow races off to follow the doctor. Shadow immediately runs into Amy Rose, who reports that Cream and Cheese have become lost somewhere in the castle. Finding the rabbit and her Chao, who have both somehow managed to get themselves stuck behind false walls, serves as the Hero mission. Alternatively, Shadow can acquiesce to the demands of Eggman's Drone and light five giant lanterns, which are in some unexplained way a part of the Doctor's defense strategy. The player can choose to chase Eggman, help Amy find Cream and Cheese, or help Eggman fend off the Black Arms. Whatever Shadow chooses, he and Amy exit the stage to find the grey Chaos Emerald abandoned on one of the battlements. The black hedgehog picks it up, only to be waylaid by Eggman in person, riding his newest killing machine, the Egg Breaker. While Shadow protests that he has no quarrel with the Doctor, Eggman isn't about to let a Chaos Emerald get snatched right from under his nose and launches into battle with Shadow.
The following weapons can be found in Cryptic Castle:
After using the first balloon, grind up the rail to the top portion of the castle. Walk along the roof to the left to get the key that is on a ledge.
After the fifth Checkpoint, the player will use the Spin Dash to get to another part of the castle and end up near a balloon. Before the balloon, the player must backtrack a bit, and at the end, kill the Black Arm soldier to open the box containing the key.
After the fifth Checkpoint, you will open a door by lightning torches. Walk down the hall, break the wall to get into a larger room, and break the wall on the right to reveal a chamber containing the key.
If the player follows the route to complete the Dark mission, they will ride a Black Hawk. The key is located in mid-air on the right side.
The final key is in the Giant Walker chase section, where it is on the left rail just before the player is launched to the goal.
Light all giant lanterns!
Light the 5 giant lanterns.
Shooting Chao or Cream will boost your dark gauge.
A shortcut through the level and a Magnetic Barrier to collect rings easily.
Cryptic Castle is rather unusual in that both Amy and Dr. Eggman encourage Shadow to kill the Black Arms enemies and scold him for destroying Eggman's robots. This means that going against the advice of a companion character (in this case, Dr. Eggman) will earn the player more points for their mission.
This is the only mission in the game where Amy appears as a partner.
If Eggman accompanies Shadow to the end of the route for completing the Normal mission, he will state that he was unaware of not only the underground rail area, but also the Giant Walker within.
If a second player controls Amy, her attack sounds are from the original Japanese version.