Unless masochism is your thing, release the Guide Bot at the earliest opportunity. Once released, he can take you to nearly anything in the mine. If he gets on your nerves, you can always tell him to scram; it is a whole lot easier than going back to get him when you are already lost. Oh yeah, give him a name (Option-Shift-F4)...robots need love too.
Set one of your cockpit screens to show the Guide Bot’s video feed. His advance scouting comes especially in handy since he has no qualms about leading you into massive enemy ambushes.
When cloaked TURN OFF YOUR HEADLIGHT! If the enemy cannot see you but can see a disembodied beam of light shining down the shaft, they WILL shoot at it.
Once you have developed a good array of weaponry, be sure to dump a mid to high-level gun and some homing missiles at your entry point to the mine (this can be done with Shift-5 for primary weapons and Shift-F6 for secondary weapons). This way, if you get destroyed you won’t have to fight your way back to your lost power-ups with nothing but a Level 1 laser and a couple of concussion missiles. This is a particularly good strategy when you come across a weapon you already have. You could take it and get an increase in ammo (if it’s a Gauss or Vulcan cannon) or energy, or you could go back and dump the one you already have at the entrance and pick up the new one later.
Leave markers at locked doors. You will be surprised how easy it is in these convoluted mines to forget where you have been. Also, the automap is not always useful for determining locations so it is nice to have a big glowing red dot to highlight your destination.
Learn early on how to use your slide controls. It is much safer to slide from around corners to shoot at a formidable foe, ducking back for cover than to just sit there and shoot at each other.
The most effective way to kill the Thief Bot is to corner it. Find a room with only one door and wait for him to show up. If you can trick him into the room, you can just sit in the door and whollop the little pest until it dies. It will not attempt to attack you or push its way past. For some reason, when the Thief Bot is intent on going somewhere, you can stand in its way and, instead of running from you, it will wait for you to move. When this happens, fire at will! It does not happen often, but you should take advantage while you can.
One nice thing about the Thief Bot is that it has keys to all the secret doors in the mine. If you can follow it closely enough, you might get into restricted areas otherwise closed to you.
The Thief Bot is programmed to follow you and do everything it can to get behind you. It will (except as noted above) retreat the instant you turn your ship’s nose towards it. To deter its thieving ways, you might want to set one of your cockpit screens for “rear view” or make a habit of doing “Crazy Ivans”, abrupt turns at random to make him retreat.
Use your flares to open doors, especially when you are running low on ammo/energy. Flares use far less energy than your primary weapons and they work just as well on doors and control panels.
Do not turn off Guide Bot messages. Most of what he tells you is unnecessary (i.e., “Looking for Red Key” or “Coming Back to Get You”) but when you have left your headlights on in a well lit room, the Guide Bot will inform you so that you can save precious energy.
When you enter the mine and find the Guide Bot, set him to find the Energy Center first. You WILL need it and it is good to have it on your map as early as possible. Second, tell the Guide Bot to find the various keys. Then find the reactor, but do not assault it yet. First you should find and clear the way to the exit. This will make a speedy retreat much easier and reduce damage by bots lying in wait for you. Once you have done everything you care to do in the mine, go find the hostages. You should do this last because, if you die, they die. Dead hostage are not regenerated they, and the points they represent, are lost for good. Once you have done all these things, you can attack the reactor and get the maximum possible points.