Shadow wanders through the forest after his last mission, back to introspecting about his identity just as he did at the very beginning of the game. Once again, Black Doom manifests in front of the hedgehog, though this time with a more powerful illusion - the entire world melts away as Doom apparently delves into Shadow's memory, to produce a simulacrum of the events on the Space Colony ARK 50 years ago. Watching from afar as his past self flees through the corridors with Maria Robotnik with the squad of GUN soldiers hot on their tail, Shadow listens as Black Doom further instills thoughts of hatred against humanity into the black hedgehog's confused mind.
This entire level therefore seems to take the form of a flashback; Shadow remembering what he did during the GUN assault that shut down Project Shadow. Not free of moral choices even half a century ago, Shadow can defend the ARK by killing the GUN troops directly in the Dark route, spurred on by Doom's Eye (though whether Doom was physically there on the ARK 50 years ago, or is simply inserting himself into the memory to mess with Shadow's head, isn't clear), do as Maria says and heal the injured ARK researchers by bringing healing units to them, or take the neutral route and simply escape with Maria as fast as possible.
Whichever course Shadow chooses, his and Maria's escape after the level is blocked by the GUN Heavy Dog boss.
Exit the starting room and activate the elevator. Get in and go to the upper level. When the elevator descends, get on top of it and jump to the key when it rises again.
You will enter a long sloped hallway where you can flip a piece of floor onto a GUN Beetle. Spin Dash up the incline and then jump to reach the key located on the catwalk.
When you reach the first Bomb Server, destroy the cracked wall to the right to reveal the location of the key.
Enter the fan room after the Second Checkpoint, and use the pulley to get to the upper level. Use the wind from the fan blowing up there to reach the key.
Continue up the elevators after the Third Checkpoint, and when you reach the room with green containers in the right corner, use them as a stepladder to the rafter above. Destroy the containers, and the key is behind them.
At each checkpoint, you should have this many GUN soldiers defeated:
Checkpoint #1: 14/60, Checkpoint #2: 19/60, Checkpoint #3: 35/60, Checkpoint #4: 45/60, Checkpoint #5: 50/60. The last 10 soldiers are after Checkpoint #5.
The player is in a maze, so the player is going to need a planned path in order to get through. Grab some weapons in the first room, and in the following room, Slide under the door to reach checkpoint 1. In the next room, defeat the four GUN Soldiers, and go through the door to find the Doom's Eye. In the next room, Soldiers will break through the walls on either side. Defeat them and continue forward. At the end of this hallway, Grab the bomb out of the Bomb Server, and use it to blow up the Cracked wall on the left. Go through the door defeat the soldiers and touch the Checkpoint 2. In the room with the elevator, destroy the three GUN Troopers in the room, and activate the elevator so that the player can go up. Continue taking the elevators to the top portion of the area of the facility, and destroy all the GUN Soldiers. The player should have 26 defeated at this point. Once that is complete, go back to bottom of the room with checkpoint 3, and go through the door on the right side (While facing them). After going through the door, the player will eventually reach a room with a bomb server. Use a bomb to destroy the cracked wall. Next, make your way past the fans. After the GUN Trooper and soldiers that come out of the wall before touching checkpoint 4. If the go into the opening where the soldiers came out of, the player will come to a point where the player need to Triangle Jump across. At the end near a wounded researcher is a switch that activates the elevator. Go straight trough the next door, and when you come out to a fan area, go right through the door. Run down the ramp to the next area. If the player would like to set up a new Checkpoint, it is located directly ahead through the broken wall. In the area with three flying GUN Beetles, use your Homing Attack to bounce off them to reach the other side. After passing through the door into a room with giant fans, go left through the door to reach checkpoint 6. After the sixth checkpoint, the player will enter an open room. This room has four GUN Soldiers in it. Go through the other entrance to defeat two more GUN Soldiers. Activate the switch for the elevator. The Player should has defeated 56 GUN Soldiers when the player get on the lift.
Tips: In this mission the player want to use speed, and that means as many shortcuts as possible. In the room with Checkpoint 2, the player will want to activate the lift, and get the grenade Launcher out of the GUN Container. This weapon is capable of destroying the cracked walls. Use the Grenade Launcher on the cracked wall below, destroy the GUN Trooper, and with its weapon, continue until the player reach the long room with the two more GUN Troopers and checkpoint 4, go straight through the door, when the player reach the fan room with the three GUN Troopers, go right and down the slope. At the bottom of the slope, go through the cracked wall to the right, bounce off the three flying GUN Beetles to cross the gap, and go through the door to enter another fan room. From that fan room, go to the player left through the unlocked door. The player will wind up a room with a lift. Ride the lifts all the way to the top, and in the final room, the player will reach the Goal Ring. If the player has avoided confrontation, the player should finish in less than three minutes and get an A ranking.
The Heal Units are usually close to the researchers they are intended for. Also, if unlocked, the Heal Cannon works just as well, if not better.
The first Heal Unit and researcher are in the first room.
If a Heal Unit is used on a GUN troop, they will stop attacking. It will also help Shadow fill the Hero gauge.
From the first researcher and Heal Unit, continue into the next room, and slide under the wall to get to the next area with Checkpoint 1. When the player goes through the door, The player will ends up in a larger room. This room has a Heal Unit and two researchers
Exit the large room with the two researchers, and go through the other door. The player will arrives in a new area. Go left and some GUN Soldiers will bust through the walls on either side. Don't worry about where they came from! Go through the door instead. At the end of the path, the player will find a Bomb Server. Use the bombs to destroy the cracked wall on the left, and go through the door to reach another long room with a Heal unit. The injured researcher is behind a cracked wall just left of the Heal Unit.
Just go straight through the door past checkpoint 2, and the player will find a researcher. The Heal Unit is located to the left guarded by two GUN Soldiers.
After entering the open room with green rail, activate the elevator by touching the switch and go up. This path will eventually lead to a dead end, but the player will find a Heal Unit and two injured researchers.
Return to the bottom of the room where the player hits the switch for the elevator , and go through the door on the right. Slide under the opening, and in the next room is an injured researcher. The Heal Unit is on the other side of the moving platform.
After rescuing the eighth researcher, go back to the side with the Heal Unit and the Bomb Server. Use a bomb to destroy the cracked wall. This will lead to a series of fan areas. When the player gets through these areas, go through the door on the right. The player will arrive in a long room with two GUN Troopers. Destroy the Two GUN Soldiers that burst out of the wall, and heal the researcher within. To get to the final researcher, the player must triangle jump across the gap further ahead.
Tips: Shadow's Homing Attack is required for the first part of the battle in order to destroy Heavy Dog's guns. After the first gun is destroyed, it becomes a usable 4-Shot RPG. The 4-Shot allows multiple lock-on targets at once. Ammo for the 4-Shot comes from destroying more of Heavy Dog's weapons.
Behind the Secret Door
A switch that will open a cage containing a single ring, once the ring is collected and Shadow steps on the base of the cage, it triggers the platform next to it. To get it to start moving, stand on the platform and follow the path and it will take you through the stage. A big shortcut helpful with the Normal Mission.
You can also trigger the switch of the cage to make the platform start moving without opening the secret door and activating the switch inside. Use Shadow's Punch, Punch, Kick combo in front of the cage.
In the cutscene before the level itself, the scenery is actually different depending on which level the player went through before, Prison Island makes the forest all green, Cryptic Castle makes the forest all red.
This stage is a more violent and tense version of Lost Impact.
This stage has more GUN troops to defeat than most dark missions.
During Expert Mode instead of reaching the Goal you must heal all ten researchers instead. Unlike within the hero mission though, they are all located in one room at the very end of the level, very close to a Heal Unit spawn.
While playing the Hero mission and running down a slope, Maria comments that Shadow used to race down the slope often. This is the only known mention of what Shadow may have been doing when not solving a problem or spending time with Maria.