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 world's smartest man is probably a good person to interrogate about his origins, he races off to follow him. 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. 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 the Egg Breaker.
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, you will use the Spin Dash to get to another part of the castle and end up near a balloon. Before you grab onto the balloon, backtrack a bit, and at the end, destroy 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 you are going down the dark route, you will find yourself aboard a Black Hawk. The key is located in Mid-air on the right side. Be sure not to miss it.
The final key can be found if you are taking the normal path. While you are grinding down the rails, and the Giant Walker is chasing you, the perspective will change so that you are grinding toward the Camera. The key can be found on the left rail just before you are 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 you to kill the Black Arms and scold you for killing Eggman's robots. This means that going against the advice of a companion character (in this case, Dr. Eggman) will earn you more points for their mission.
Despite the fact Amy is a hero character, she attacks the Egg Pawns, earning the player Dark points. This is especially ironic as Amy will scold the player for defeating them, despite being the one doing it.
If Eggman accompanies Shadow to the end of the neutral route, 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.