Find Factory Computer
After you reach the factory, you'll have to blow through a vent cover, crawl through a set of conveniantly-big-enough-to-move-around-in ventilation shafts (send your troops on ahead of you, as the last room here features a large group of battle droids), then blow or slice through another door to reach the factory computer.

You'll need to be ready for these SBD's if you want to get through the door here.

Now, you can feel free to go ahead and slice the computer, but be advised that doing so will open the force fields near the other door in this room. Behind one of these fields are a pair of Super Battle Droids, and you're going to have to take them on with only two squaddies at the outset, since one of them is going to be slicing the console (unless you want to cancel the slice as soon as the fields drop, of course). Obviously enough, EC grenades are going to be a big help here, since there aren't any sniping positions, so you might want to just command your squaddies to stand directly in front of the droid forcefield before slicing the console; the droids will automatically target them, allowing you to throw a couple of grenades their way without fear of getting blasted. The grenades will effect your squadmates as well, of course, but there aren't any other enemies to worry about here, and you'll have a bacta tank at your disposal as soon as the SBD's are dead. If you're running low on EC grenades, then you can find a box of them next to the bacta dispenser.

Destroy First Power Conduit
After the computer's been sliced, you'll be able to blast through the far door of this room; another SBD is awaiting beyond, but you shouldn't need to use an EC grenade on it if you place a soldier at the sniping point. Even if it does deal a bit of damage to you, it's a short walk to the bacta dispenser, so don't waste any ammo you don't have to.

The Elite laser can do a number on the battle droids you encounter in the factory.

Where you are going to want to use an EC grenade is in the hallway beyond the door behind the SBD; there's a small army of battle droids here who'll become sitting ducks if you hit them with a grenade at the right time. After they're dead, take up sniping positions to cover the soldier who has to slice the computer on the far end of the room. When it's down, you'll be able to grab a Geonosian Elite laser weapon from the small antechamber that opens up. This is going to be your SBD killer for a while now, thanks to its immensely powerful beam. Unfortunately, it only has a limited amount of ammunition, and the amount remaining isn't displayed on the weapon, so you won't be able to use it without reservation. When it runs out, it'll be discarded; you probably have around 20 seconds or so of pure beamy goodness to work with, though, which should be enough to cut down a few baddies.

After you retrieve the laser, start making your way down the ventilation shafts until you come to a room with a murderhole overlooking an SBD. If you concentrate your squad's fire on the baddie, then switch over to sniper mode and start blasting it, you should be able to kill it without resorting to laser fire. After moving down the ramp, you'll come to the first power conduit, which is an obvious target for an explosive charge. Be careful, though, as its detonation will trigger the appearance of more droids, including another SBD. Feel free to use your laser on this one, if you wish; you can afford to be a little reckless since there are more bacta dispensers beyond the fallen force field.

Destroy Second Power Conduit
After the destruction of the first power conduit, you'll have to move on and destroy another one before the factory is shut down for good. To do so, open the door near the bacta dispensers, kill the battle droids, then place one of your soldiers at the sniping spot off to the left, near the ammo cache. This soldier will spot a pair of SBD's coming your way through the hallway nearby; this is a perfect spot to use your laser or EC grenades. When they've been blown, though, you'll be able to move another soldier to the sniping spot in the hallway, giving your third squaddie plenty of cover while he slices the forcefield leading to the power conduit.

When you've sliced the forcefield, the same squaddie can be moved around the corner to place a charge on the conduit itself. When that's done, blow it, then withdraw back to the bacta dispenser to heal your soldiers up before moving to exit the level through the ventilation shaft near the conduit.