Right next to your squad at the insertion point will be the Scouter. You can use it for drive-by tactics, but it can only hold two people at a time and, depending on your squad, it may be better to just proceed on foot. The map consists of a long road in a zig-zag pattern. Following this path will have the most resistance by super mutant forces, but the off-road shortcuts tend to be minefields. If you do decide to take the shortcuts, you should have a squad member with an adequate amount of Traps skill.
The first generator is relatively unguarded, just a few super mutants patrolling.
Further down the road the second generator, which will have automated Gun turrets guarding it along with a few super mutants. There is a small door on the left side of the fence which makes it possible to either sneak past or run past the one turret on that side and avoid fighting them altogether.
The third generator is in a makeshift fortress of fencing and sandbags with quite a few more super mutants than the previous generators. Shooting through the gaps in the fencing will take care of most of the melee Mutants, and the rest can be dealt with either from a distance or using cover. Once the third generator is destroyed it will open the two large black doors to the factory. Inside will be a Commander who will not initially be hostile, but after a speech, will attack wielding a cattle prod.
The fourth generator is inside the Factory, completely unguarded. The factory, as it turns out, is not a weapon's manufacturing plant at all, but a research facility trying to cure the super mutants' sterility problem. You are now given the choice of either destroying the research or leaving it for the BOS to capture to use as a bargaining chip. Once you decide, the generator is in a room upstairs, once it is destroyed, follow the fire escape to the exit grid.
The map on your Pip-Boy will indicate that on the north east side there is an underground tunnel to the factory, but this can be ignored as it turns out it has been filled with rubble and debris, it is also guarded by a single super mutant with a Browning M2.
If you decide not to use the Scouter but would like to take it with you, exit the mission as normal, then re-enter Jefferson. You will arrive at the original insertion point next to the Scouter which you can drive out of a grid right behind you.