I remember being utterly confused by that bit too but I haven't played it for years and don't have the disks anymore.
This is from the walkthrough. Good luck!
3.4 - Pearl Harbor 3: Starting
Right after you dive into the water, and head into the bottom of the ship,
there you are. Turn left from where you start and take a few steps, note
the ladder is covered in flames, so it would generally be a bad idea to try
and climb it, but look right and voila, an opening. Take a peek through the
crack in the wall to observe a few midshipmen trying to save the ship, the
boiler explodes, and punctures a hole in the wall to your right. Take that
opening and as soon as you get through, another boiler explodes in a guy's
face, look right when that happens and you should see a glowing red
valve, run over there and hold the USE key to turn it off, which will shut
off the flow of hot steam that's flowing from the boiler, now run to the
back left of the room, where another explosion occurs, look right, and climb
the stairs, when you get to the top, look for two small red valves on the
pipes, turn them both off, then cross over to the opposite side to do the
same to another valve. When you're done, proceed into the next compartment,
down the catwalk to the end, look right, and go all the way down the stairs
into the flooding chamber. Swim over in the direction of the floating body
to shut off the first steam valve, then after you do, look right and turn
off the final big valve (where the two corpses are). After you shut it off,
follow the sailor up the stairs and into the next chamber, as you see for
that sailor there, it might not be a good idea to go in that door, look
right and go down the two steps and look right again to go up the flight of
stairs you're supposed to. As you get up the ladder, there will be an
explosion in your face, don't worry, look right and head over to where the
midshipman is standing, follow him down the corridor and into a room that is
on fire with a couple of sailors fighting the fire. Grab the ax on the
wall, and chop the top of the oxygen tank to send it flying into the damaged
door. Keep crouched so you don't take damage from smoke inhalation, and
head on through into the next room, meet up with the medic in the center,
and he tells you to bring the injured to him. Look left, and you'll see an
ailing troop, you know what to do, go grab him and set him down next to the
medic. Head on through the door to the right of the firefighting sailor,
and hug the left wall to avoid the steam from the first jet, then with your
ax, chop the red portion of pipe, which will allow you to pass without
taking damage. In the next room, you can hear a soldier call for help, and
you NEVER leave anyone behind, head on over to the back left hand corner of
the room, pick him up and take him back to the medic you just walked past at
the entrance. Look to the east side of the room, to where the broken door
is, help him out by hacking the door a few times with your ax to open it up.
In the next room, walk forward, and then take a right, use your ax again to
chop up the boxes that block the path to the ladder, and then take it up.
When you reach the top of the ladder, you'll be at....
3.6 - Pearl Harbor 3: West Virginia Deck 2
make a left and move straight on ahead, in the next fire-filled room, take
a right and in that room, move left, and you'll see a sailor have a whole
bunch of boxes fall on him, take your ax and use it to break the boxes that
fell on him (don't fret, you wont kill him), pick him up and go through the
door forward and to the right of where you just entered the room you're in.
Move with the sailor to the end of the corridor, near the stairway, but not
too close, look left, and there will be a medic, drop the soldier you're
carrying, and when the medic asks you if there is anyone left behind, you
tend to think there is (plus, you can hear someone calling for a medic). So
backtrack down the corridor, and on your right you'll find a broken door
that you can break open with your ax, and then lo and behold, a commanding
officer was trapped. Do the same with him, take him back to the medic.
After you rescue him, head towards the staircase leading up right in front
of you, they'll clear the way, and you'll be on your way to the next part of
Pearl Harbor!
3.7 - Pearl Harbor 4: Starting
Right then, you're topside now. When you start, head towards the bow of the
ship, and then hook a right to get to the opposite side of the ship of
where you started. Hump over towards the stern, and you'll see someone call
for help on the guns, there's your cue! Head up the stairs and man the
machine gun, where he is already stationed as a spotter. You know what to
do from here, you have to protect another ship as it makes a run. Again,
its all Jap aircraft, so show them what for. Keep firing until somehow the
gun explodes, and you're fine. Look right and man an anti-aircraft gun a
few spots down, and again take aim as best you can, just keep shooting down
planes until the Japanese start retreating. Mission over.
:salute:
