There are multiple objectives for the player to do before completing this level. Upon arriving, the first objective must be done before proceeding. After reading the terminal, hit the left switch on the wall to reactivate the power and life support systems. Take the lift up and grab the goodies, powerup and then save.
The next objective is to free the four elders. To gain access to the stasis control ride the far left stasis chamber lift up. After hitting switch, jump down through one of the stasis chambers and at this point you'll notice the remaining elders activated and fighting with you. The next room requires a switch in the control to be activated before the switch in the main room will work. Take the stairs down and head for the large central core.
The easiest way to navigate the core area is to go to the left wing and run/jump to the ledge on the left. Down this hall you'll find a closed locked door. Head back to the ledge run/jump to the center ledges, continue running through the center 'thing' and head for the lowest ledge on the opposite side of the tank.
Enter the blue cooling tank area which turns into a battle arena under the watchful eye of your hunter. Unfortunately, you can't end the battle here because the blue Hunter gets away and there is nothing the player can do to stop this. Continue to explore the cooling tube areas until you find yourself at the large central core again. Looking ahead you will see a 1x powerup. My suggestion is to ignore this powerup for now, it will become available later.
Run/Jump to the left ledge (the one with the close door you visited earlier) and head into the small goo tank with four platforms. To exit the tank it's just a matter of riding each platform up until the top is reached. The top switch will lower the platform you are on as well as the goo in the tank. At the bottom the goo in the middle of the tank contains a 3x powerup at the bottom.
Entering the now drained central tank, you will meet again the blue hunter. This time you will need to battle the hunter. After taking care of your hunter hit the switch outside the center elevator. Once the ledge with the powerup comes down, walk inside and ride the center platform up to the walkway.
Once outside the ship, shoot the switch across the way to raise the triangle wedge platform barrier.
Continue on through the ship, jump down the shaft at end of the curved goo corridor and walk out into the large outdoor tank. The lit alcove to the right before entering the large tank will teleport you to a small high above tank where a 1x powerup is waiting.
Go through the tank area into a room full of control panels. ride elevator up and hit switch, which will open door on opposite side. Walk along the rim of the large tank and re-enter the ship. Your next objective is to regain control of the ship's bridge and the only access to the bridge is a secret passage used by the ship's captain in the event of an emergency. To reach this passage you must go to the upper most part of the ship (the upper deck) and find the captain's secret lift.
To activate the platform to get to the upper deck hit the switch inside the triangle shaped veined room.
Take platform to deck and prepare for some battle. At this time take note of emblem on flags-the enemy's colors!! Now that your blood is boiling, continue to the center room on the deck. Inside is a switch that will give you access to the captain's secret lift at the far end of the ship.
Once inside the Captain's ready room enter the room with three friendlys. They will go into action once you enter the bridge through the other door. Eliminate all the baddies on the bridge and walk up to the red projectile coming out of the right horizontal control panel. Hit your action key to reset the ship's computers.
After the computer is reset the door exiting the bridge will open allowing you to ride the platform back up to the top deck. The final objective is to restore flags colors and to do this just hit the nearby switch. Ride lift down to the armory and load up on ammo and prepare to teleport out.