The "Right" Way
This is gonna be in a big firefight. Before the mission make sure you have the proper equipment such as armor and good firepower. First take cover behind the gate (the bullets can't go through unknown reason) and use your M4 to take the guards out. Then head on and beware of the sniper on the catwalk and the man behind the crate. There will be a van with about a dozen guards, there should be two explosive barrels, blow them up causing a chain. Then sprint and take cover toward a box there will also be several behind a stack of boxes two will be firing while one will be hiding and two people will be hiding further. Take the close people out then move quickly to the farther ones, if you are low on armor there should be an armor pick-up. Then there will be a squad of men by the staircase throw a grenade or molotov (if you have none use an RPG) and move on. You will head on top of another roof, here use the health pick-up and move (little resistance). There will be two or so people coming down, shoot them before the hit you. Head up and once you see the ice-cream swirls, there is one guy hiding be quick and kill him. Then you head up to the exchange, BEWARE WARNING: YOU WILL ENCOUNTER AROUND A DOZEN OR MORE MEN HEAVILY ARMED AND HIDING. Throw a grenade, molotov, or shoot an RPG at the middle between the two pillars. Shoot a couple of times at different angles and then (BEWARE THERE MIGHT BE SOME SURVIVORS) move from the side, not between or you'll be cornered and eliminate the rest. If y ou are low on health, exit the battlefield and head toward the hospital nearby and then continue on. Once they are eliminated it's pretty self explanatory from then on.
The Alternate Way
Doing this mission the "right way" can be very costly to your bullets. The factory backyard is infested with a flock of enemies and clearing the whole place will most likely be both ammo- and time-consuming.
There is a fast way out of this, which saves your ammo and especially your patience. Arrive at the payphone with a helicopter (The Maverick on top the Vercetti Estate would be the nearest one) and start the mission. Use your helicopter to land on the nearby building on the left side of the factory (assuming that you are flying from the payphone's direction). Snipe every single enemy on the roof where the briefcase is. This allows you to sprint-jump on the factory's roof with no lethal force ahead, picking up the briefcase and escaping to the airport with the helicopter provided nearby, without needing to take out the gunmen at the courtyard below.