Having stolen the two Chaos Emeralds from Westopolis while ignoring both Doom's Eye and Sonic's entreaties, Shadow is confronted by a hologram of Black Doom on the city's broken streets, enraged by his intransigence. Black Doom muses that "perhaps Professor Gerald has done more to your memory than I imagined", referring to the scientist's reconditioning of the hedgehog after Maria's death. The still-amnesic Shadow is unable to comprehend the message; Black Doom responds to his sudden spark of curiosity by Chaos Control, teleporting him to Glyphic Canyon as punishment for his disobedience.
Shadow senses activity in the area, and proceeds to investigate. After a short run into the stage, Shadow will come across Knuckles the Echidna, presumably caught in the crossfire during one of his periodic treasure hunts, who wants help to 'get rid of these annoying aliens'. Still further into the stage, Shadow is once again faced by Doom's Eye, and is instructed to touch the five jewels around the stage and reawaken the temple. In an effort to activate the long-forgotten power cores buried within the temples, the Black Arms assault the ruins. G.U.N. forces scramble to hold back the invaders.
With or without Shadow's help, it seems that eventually, Black Doom manages to activate all the temple jewels. Reawakened, the temple ruins are able to levitate, and are used by the Black Arms to invade the rest of the world. Later in Sky Troops, however, Shadow is forced into a stratospheric battle between the Eggman Fleet and the Black Arms ruin-ships.
The following weapons can be found in Glyphic Canyon:
15 Black Arms should have been defeated by the time you reach checkpoint #2. There are none between checkpoint #2 and checkpoint #3. 25 should have been defeated before reaching checkpoint #4, 27 before checkpoint #5, 34 before checkpoint #6, and 44 before checkpoint #7. The remaining 16 are between checkpoint #7 and the Goal Ring.
A Black Volt will take the player to the sixth checkpoint via an alternate path. Along the way, the player will find ring boxes and a fire shield (Heat Barrier), and several extra Black Hawks, if the player is doing the Hero Mission.
This level has the same format as Sky Troops, although, lifted into the sky. It has a few differences, however.
It could be inspired by Wild Canyon, in which Knuckles was a character that helped you in the stage.
There are actually more than sixty Black Arms enemies in the stage area. If the ones behind the Secret Door are also taken into account, the number of enemies present is well over 75.