After acquiescing to Black Doom's orders and eliminating the G.U.N. soldiers in Westopolis, Black Doom commands Shadow to infiltrate cyberspace and cripple the humans' communication infrastructure, intending to plunge the world into chaos. To this end, Shadow is Chaos Controlled into electronic form inside the UF mainframe. Doom's Eye instructs him to delete the core program controlling information flow (which the player can choose to do or not), but as Shadow progresses into the binary realm, he's given a different choice by none other than Rouge the Bat. How the thief got in there too is anyone's guess, but she's on a mission to collect the Chaos Emerald that's powering the system, and asks Shadow to help.
It's G.U.N. vs. Black Arms crossfire that Shadow has to avoid again in this level, although actual human G.U.N. soldiers are conspicuous in their absence; instead the fight against the aliens is being prosecuted by G.U.N.'s robotic Beetle drones, and the crystalline antivirus programs which divide twice before they are destroyed.
Key #1: In the light speed circuit after the second Checkpoint, take the first path on the right to get the key.
Key #2: After coming out of the second light speed circuit, you will see four flying GUN Beetles. The key is located on the lower level below the entrance to the next light speed circuit.
Key #3: just after the fourth checkpoint, hang on to the light beam, and ride it up to where the key is located.
Key #4: After the fifth checkpoint in the area where you need to hit the flying GUN Robots, destroy the first three, and then land on the platform with the key. It's located on a platform near the two flying GUN Beetles.
Key #5: After the seventh checkpoint, use the searchlight to go up. Once you reach the height, point forward and use the Homing Attack to reach the highest green platform that will lead to the key.