I am having problems overcoming the robot. Before I finish planting the emp, it shoots me. See below for the part where I am stuck.

ISLAND BASE Crouch behind crates to avoid being seen by patrolling
guard Wait for him to walk the other way, then take him out with a
silent attack. Interact with console and rotate turn table 3 places in
either direction (orientation stays the same, but the direction of
travel on the conveyor is now the opposite) Step onto the conveyor ? do
not walk or run as the guard will hear you and alert the robot. Access
the pump room Use the ladder to access the raised platform Knock out the
guard Access the console Rotate turntable 2 places anti clockwise Cross
the turntable ? again do not walk or run Access cable car upper Being
careful not to wake the robot…. Access console and rotate turntable 1
place clockwise Take the emergency power pack Cross bridge to access
adjacent raised area Use turntable to access target location Keeping out
of sight of the robot, plant an emp mine. THIS IS WHERE I GET STUCK !!!!!! Hide behind crates and wait
for the robot to deactivate.

Call lift Insert power pack
Take lift down to manufacturing
Take the door to the power room
Walk around the gantry to the next door.
Lift button doesn’t work
Walk up to door button
There is a robot in the adjacent location (can walk in
and not get shot if the Remora doesn’t bleep)
Turn valve wheel to attract the attention of the technician
Talk to technician
Either let him turn the wheel, or do it yourself but don't let the technician take the lift back down to the floor below...knock him out!
Take the lift down
Run past the guards to the door on the right
Use scanner in front of the nearby door with button.
Watch out for patrolling guards
Use staircase
Take door into adjacent location - more patrolling guards
Take either door but enter the room with the guard and the recharge point
Kill the guard, insert an EMP mine
Access adjacent location and cross the gantry
Walk through door, but stand in the doorway
Shoot guard and attract robot
Run back across the gantry, into the location with the recharge point
Robot should be deactivated
Go back to the robot’s original room
Take the door on the left
Take stairs down to the door on the right
Access lift area & kill guard
Take lift down to the security session
Take the only door available into the connecting corridor
When the robot isn’t looking use the door on the left of the screen to access the interrogation room
Talk to the technician and find out where the door control room is
Use the Remora scanner to watch for patrolling robots
Access connecting corridor again
Use crates in the foreground to hide behind and wait for the patrolling robot
When he is facing in the other direction run through the door on the right to…
The security command room
Take the first door on the right.
Continue into the next room and down the stairs.
This is Alexandra’s cell but there’s no way to release her.
Go back & listen for the robot from the connecting corridor and the guard from the lift area
When all is clear re enter the security command room
Hide behind the crates (crouching) so that neither robot can see you
When the robot in this location turns to face the robot from the connecting corridor, crouch walk to the door next to the boxes
Proceed through this corridor into the door control room
Knock out guard
Access console
Select door security controls
You can not release Alexandra’s cell door (#2)
Lock door #4 when robot is in the room with crates….
This makes the security room robot come and check the door controls
Lock doors #9 & #10
Wait for robot to access previous corridor, then lock door #7
Lock door #12 when robot is not in lift area
Release doors #9 and #11 (the lift door)
All robots are now locked out of the way
Release locked drawer from console.
Wait for lift guard to be as far away as possible…
Shoot command room guard…then lift guard when he runs in
Get security pass from locked drawer
Access main lift
Take main lift down to the quayside, and see there are far too many guards
Take main lift up to the reactor level (#2)
The middle door is locked
Take the door on the right of the screen into the control room
Wait for patrolling guard to be walking away from the camera
Run down stairs and knock out guard at console
Shoot patrolling guard
Access console
Look up all information on reactor and unlock the pump room door
Back up the stairs to the internal lift in the middle of the screen
Access the area above
Talk to the technician about the auxiliary pump
Take the main lift up to the cable car docking area
Insert EMP into the recharge point
Shoot at robot to attract its attention
It will turn round and come for
you, in so doing it will deactivate itself
Access Auxiliary pump, and deactivate it with the valve wheel on the wall Return to reactor level
Go to the pump room, the door should now be unlocked
Deactivate primary pump
Quayside guards leave for the cable car docking area
Main lift is in use
Access control room & take internal lift to area above
Cross bridge to adjacent area
Use internal lift to area below
Kill guard
Take the access lift down to the quayside
All the guards have left except 1
Shoot him
Use staircase to command room
Interact with console

Hope that helps a bit!
I have actually completed this game but it was a long time ago so I searched around and found this on another website (sorry, can't mention which one it was..unless you PM me!) - possibly the same one you got your first bit from!

Thanks to Cartman for the walkthrough!