I killed the Spider Droid with the rock on the bridge before visiting the Holograph, but after he teleports me back to the surface and I cross the bridge again, another one appears, and I cant destroy it OR kill Orat. If I try to throw the water it says "Come to your senses, that couldn't help you at this time" or in the cave, it says "no time for that". and the spider droid won't follow me into the cave. So how do you get past it?

A second spider droid? That's weird...

That sounds like a bad glitch. As far as I know there should be no other spider droid. The whole point to the event is that you destroy the droid, and sarien's assume they 'got you'.

There are two ways to get rid of the droid in the game, and again there should only be one droid. The first way is dropping the rock, the second is leading it into the cave and letting the two kill each other (this is done after talking to the underground leader).

The latter gives extra points IIRC, but not entirely sure on this.

You might try reloading to an earlier point in the game, and avoiding the robot until after you get back from the underground. Then figure out how to destroy it, your choice of the two options.