So this is my first playthrough of Fallout 2 and it seems as if I need to side with either the Hubologists or the Shi. I accepted a mission to kill the Hubologist leader, but when I talked to him he asked me to kill the Shi emperor and I said okay. Then he asked me to kill Badger.

Anyway, after doing some more snooping around I decided I didn't really like the Hubologists after all and I'd rather help the Shi. However, I wanted to get some more hardened Power Armor (I'd already upgraded one set) and I assumed there would be another set to get upgraded. Long story short, I found another set and tried to go back to get it upgraded and then kill the Hubologist leader, but I could no longer get past the AHS-7 guy as there was a forcefield.

Every time I talk to him he just asks me if I've killed Badger yet and I say no and that's it. Is the only way to get back in to kill Badger?

You can disable shields using "Repair" skill. Of course, such skill doesn't work during combat. You can kill all Hubologists but Crocker (or what was that technician name). Kill all Hubologists and they'll stop asking questions... ;-)

What do I click on to repair to get it to open?

For clarification, I've tried clicking on all sorts of things, but when I click on the emitter, the only options I have are to look at it or use an item with, all of which say "That does nothing" including explosives and repair items.

Yeah, that's what I thought, but for some reason, when I right click on it the only options that are available are the "Look at" option and the "Use Inventory Item" option.

Here's a screen shot so you can see what I'm talking about.

Try the conical thing a bit lower?
Or the thing below that.

It can be tricky activating the skill when you need to point at exact correct pixel.

I tried clicking every part of it and nmever got the option to use a skill on it.

I found that I could get them to temporarily flicker by placing some dynamite in front of them, which allowed me to get in, but this required going into attack mode against all the Hubs. This wasn't a problem in of itself as I was planning on killing them all anyway, but when I went to talk to the engineer guy who can upgrade my armor he said he "had a beef with me" and he went into enemy mode.

Excuse me.
But if i remember right, it was so that you first choose your skill
and than the target.....so press *s* (skill) select repair
you get your cross-hair and than the object you want to repair.

edit: just remember the skill is no. 8 so just press 8 for repair and
than the target....foila success or repeat it.

Ah, that did it. Thanks. Seems obvious now, forgot about that.

I use the tools to get by the force field, but it's a matter of having sufficient repair skill and luck to get it to work. Otherwise, the force fields inside Hubologist base don't always have the option to use the repair without hotkeys, it's a terrible oversight on the designer's part.