The main problem players encounter here is how to open the grate shutting off some hostages from a small maintenance tunnel. To open this grate, you can go two ways. Each of them require you to obtain the blue key first. Once you have done that:
 

1. Either descend the shaft containing the blue keycard to its bottom end. Exit it into a huge hall. Leave that hall through the wide door in one of its corner with a PTMC sign above it. You enter a corridor ascending in a left turn. Follow the corridor until you pass a wrench symbol at the wall and hear the sound of a disappearing wall (do not fly too far past the wrench symbol!). Proceed with step 3.

2. Or fly the shaft containing the blue keycard back up. Leave the hall with the lava channels the way you entered it and return to the middle hall where you started the level. Fly through the wide door in one of its corners. You will enter a corridor descending in a right turn. Follow it until you reach the wide door at its other end. Turn around and fly back past the wrench symbol and hear the sound of a disappearing wall (do not fly too far past the wrench symbol!). Proceed with step 3.

3. Now turn again and descend the corridor until you reach a maintenance door located at the left wall (immediately before the wide door leading to a huge hall). Fly through that door and follow the maintenance corridor to its end. Slide up, then proceed to the direction you initially had until you reach the hostages. Pick them up and proceed to a chimney with another switch at its top.

Shoot all the animated switches and symbols scattered throughout the level to unlock the various doors and shut down the force fields. Some switches are located at the very top of the chimneys found in the level.

Simply fly through the grates they are behind to rescue them. There are no other secrets in this level.

Fly past the reactor room and descend into the 'control center' below. The switch located at its backside opens the first force field in the reactor room. Destroy the mini reactor now visible and shoot the switch below it: It will shut down the second force field. Proceed until the reactor force fields are shut down.

Fly through the grated door in the first room. You will enter a triangular room with accesses to three mini reactor rooms. Only one of these rooms is accessible at this time. Enter it, destroy the mini reactor and shoot the switch below it: This will unlock the first arsenal's door. Enter the arsenal and shoot the image at its rear wall: This will unlock the second mini reactor room. Proceed until all arsenal doors are unlocked.

The earth shakers are hidden in two water-filled tunnels at the bottom of the level. Their access is blocked by grates. To remove the grates, enter the middle shaft in the huge triangular boss room. Shoot the trigger at the ceiling of the shaft to open the grates.

From the hall you started, proceed to a half-sperical hall and kill the water boss there. The 'island' in the room's middle contains a short tunnel covered by a grate you can pass through. The switch at the end of the tunnel opens the walls blocking the access to the yellow key card. To retrieve it, return to the central hall, fly through the water to the right of your start position and follow the tunnel until you reach a deep 'well'. Find the yellow key card at the far side of that room.

Hit the switches at the ends of the tunnels containing the earth shakers with guided missiles or the phoenix cannon.

The only way to leave the room where the yellow key card resides has a side tunnel hidden behind a fan which can be passed through. Follow that corridor to its end to find the secret exit.

There are no secrets I know of.

In the corridor with the three grated bridges, pass all bridges, than return to the shaft you came from flying above the bridges. This will open the grates blocking access to the gauss cannon.

Descend into the volcano in the final boss room. You will enter a circular room with a deep lava pit. At the bottom of the pit a switch is hidden. Destroy it with a guided missile to open the grates in front of the earth shakers.

At the back of this room there is a flickering light. Behind it, there's an inaccessable small room with a trigger at it's rear side. Shoot the trigger through the light to open two of the grates at the opposite side of the hall blocking the access to the room below.

Between the outer four of the stalagmite/stalaktite pairs found in this hall, there are robot generators (matcens). They are triggered by switches at the middle stalaktite as well as around and in front of all power ups found in this hall. You can avoid the switches by flying between the stalaktites. Most switches trigger two matcens at a time. Be very careful not to pass too many triggers at a time, or survival will become a rather impossible task!

Two of the golden panels are hidden doors. You need the yellow key card to open the hall's exit door. The yellow key card as well as the trigger to unlock the next door are found in a small room behind the other hidden door.

Before killing the boss bot, make sure to kill all bots at the shafts originating from the boss' pits rear end. The exit tunnel is extremely long and covered with lava which will damage your shields when you touch it (and avoiding touching it after killing the boss is a tad difficult as the whole level is shaking). You might want to save the invulnerability found in the shaft above the boss pit's matcen for this occasion.