After either assisting Charmy Bee in stealing the five disks on Prison Island, or simply retrieving the Chaos Emerald from Circus Park, Shadow enters a part of one of Dr. Eggman's bases, and runs into Team Chaotix while they are trying to hack Dr. Eggman's computer. Shadow assists them in hacking the computer (by smashing the keyboard), and goes into the cyberworld himself, just before Espio goes in. Shadow finds himself in the Blue Network of Eggman's Mad Matrix, and plans to go to the core because he believes "the Doctor must know something". Inside of the Blue Network, Espio asks Shadow to help him extract data from all four terminals. Just outside the blue terminal, Doom's Eye informs Shadow that bombs have been set along the circuitry and instructs Shadow to detonate them all, as this will destroy the Doctor's mainframe. The player can then either choose to help Espio re-activate the computer terminals, escape the cyberworld, or help Doom's Eye destroy the cyberworld.
Throughout the level, Espio instructs Shadow to leave the Egg Pawns alone, lest they attract the notice of not just antivirus programs, but Eggman himself. Regardless of the route Shadow takes, Eggman eventually ambushes the intruders with his Egg Breaker.
Tips: Throughout this stage you will see colored tiles. When you step on a tile, it will change colors. To trigger the mechanism that they are attached to you must match up the colors. The color pattern Changes as follows: Yellow, Green, Blue, Red, Yellow. After the first Checkpoint, ride the beams of light up to the top of this tower. Make sure you get the weapons from the Egg Pawns, because you will need the gun to shoot the colored tiles and match them up. Once you reach the end of this section, the blue terminal will be activated. Activating the terminals does not matter for the normal mission, but it is good to know where you started so that you don't find yourself backtracking.
The Goal Ring is inside the Red Tower. That is where you will be able to escape. Once you are in the main chamber with Goal Ring, use the wind to float over to the right or left side with Egg Pawn, and step on the colored platform. When all the colors line up, you will be taken to the Goal Ring.
The Yellow tower: After the third checkpoint, you will jump across to some rising and descending blocks. Just past those blocks is another platform with different colored blocks. Turn all the colors at the top, and Light Dash to the exit of the tower
Green Tower: The first couple of sections in this tower are pretty easy. You must match up the colors in order to remove the barriers. After getting by the Black Hawks in the beginning section, you will see a long, straight path hovering in the air. Remember that the colors change in a certain order. Jump onto the yellow and change them all to green. After the platform rises, you will arrive at the fifth Checkpoint. The next mechanism that is activated is a moving platform. While you are on the platform, you must shoot one of the colors that remove the barrier ahead. Jump off the platform and get ready for the next section. Get a weapon out of a container, and activate the next platform. You will need to shoot multiple color Tiles while the platform is moving. Don't forget that you can move to the side while aiming froward by holding Down the R button (GC), R Trigger (Xbox) or R1 Button (PS2). When you see the color tiles on the floor, jump off, and line them up to make that platform rise. You can also use your Homing Attack on the spring for a faster route to the top.
Red Tower : After entering the Red Tower, you will see a bunch of Colored tiles and Egg Pawns to either side. Match the colors tiles to raise the platform, and Triangle Jump between the blocks to reach the other side where the Light Speed Circuit is. In the large area after the Light Speed Circuit, float up to the top using the large wind column, and make your way to the center area above the large sphere. Don't touch the Warp Hole, or you will be sent out of the tower.
Tips: Use the springs around the area to reach the higher level above the boss, where there are Egg Pawns with Egg Guns. The Egg Guns are more effective on the Egg Breaker than the Egg Pawns' RPGs in the bottom level. Also, using Chaos Control can quickly finish him off.
The Secret Door is located on the two-toned 'mini-tower'. inside is an alternate and much quicker route leading directly to the Red Terminal. Absolutely nothing along the way.
Although Espio is the partner character for the Hero mission, he will attack and defeat the Egg Pawns, earning the player Dark points. This is especially ironic as Espio will scold the player for defeating them, despite being the one doing it.
In this level (in Expert Mode), instead of going straight to the goal, the player has to activate all the terminals like in the Hero mission. This is probably due to the goal being too easy to access.
Also in Expert Mode, Omega "challenges" the player to access the terminals instead of wishing Shadow good luck like every other character via hint ring.
During the boss battle, if the player destroys Egg Pawns, Espio tells Shadow to stop because they may attract the attention of Eggman, despite the fact that Eggman clearly already knows that they are there.
In the opening cutscene for the stage, Shadow will hit the computer to get it to work which succeeds. Charmy Bee would later replicate this in The Last Way to the same result.