Go through the doorway south and up the stairway. Get a Yellow Herb and Shotgun Shells from the crates here. Also get "Our Mission"; it's Saddler's plan to take over the U.S. government, which we've put a stop to. But there's a backup plan where Saddler will use the parasites to cause so much chaos that the government will fall. Once he's in control of the U.S. he'll be able to take over the world.
Go through the door here.
You're outside again. There is one final typewriter and chance to talk to the Merchant. Collect the items here before going down the stairs. There is a Green Herb and two boxes. Talk to the Merchant to make final preparations. During the upcoming battle you will need to pick a certain item and you will need to make room for it. You don't have to go overboard because you will be using items in the battle, but it's best to have six or eight free squares. If you're low on health times then get some First Aid Sprays; sell Shotgun or Handgun Ammo to make room if you need to. Make any last minute tune-ups to the weapons you're going to use, then save.
Go down the stairs to start a cutscene. You sense trouble so you leave Ashley behind and take the elevator up to the docks. There you spot Ada, alive but tied up and hanging from a rope. Saddler is there and he tries his Jedi mind trick on you but realizes it won’t work anymore. You free Ada with a throw of your knife and Saddler undergoes his final transformation into a parasite based monster.
If you think that it’s time for a final cutscene followed by the credits then you're sadly mistaken. There is a cutscene though.
The "sample" that Saddler's been carrying around is left behind, miraculously undamaged. You pick it up but Ada comes up behind you with a gun and forces you to hand it over. She makes her escape by jumping into a passing helicopter, but not before giving you the Jet-ski key. She also activates timed explosives which will destroy the island in 3 minutes. You have that amount of time, minus whatever is used up in cutscenes, to make your escape.
Cross to the east dock if necessary and head north to the elevator. (This was locked during the battle.) Grab Saddler’s 100000 PTAS drop as you go by. Take the elevator down and watch a cutscene showing you and Ashley heading into an escape tunnel. (This is the second cutscene which eats up you time, but you don't get any benefit from skipping them since the game just advances the timer by the amount you skipped.)
Follow the tunnel, there is one point where you need to drop down then catch Ashley. (No, you can't leave her on the Island.) Locate the jet-sky at the end and use the key to climb aboard. Use the analog stick to steer and accelerate.
You must now get though some dangerous caves, in fact you may find this more difficult than the boss because mistakes are punished by instant death. There are three spots where a iron bars block one of two arches, go right first, then wait a bit, then left and right. You go over a jump and explosions start. Now a wave is following you and you must accelerate to stay ahead of it. Keep dodging left and right to avoid rocks, and aim for spots where you can jump the jet-ski over trouble. Fortunately you can't run into the walls, only obstacles, so that makes the steering a bit more manageable.
Eventually the final cutscene starts. You come flying out the side of a cliff and land in the ocean. Ashley falls off but you quickly pull her out of the water. Ashley ask if you'd be interested in doing a little "overtime" once you get back but you turn her down. You ride off into the sunset and the credits roll.
After they're over you gets a call from Hunnigan who can finally get through. You report your success and hit on her while you’re at it.
You may be wondering what is the point of having the final boss drop money. When you compete the game you get a chance to save, which will be labelled New Round/Cleared Game. If you then load this save you start a new game but you keep all the items and equipment you had after defeating Saddler. The game starts with a shopping session with the Merchant where you can buy new items as well any others you can afford. The new items include the Infinite Launcher and Matilda. The Merchant also carries all items and weapon upgrades anywhere in the game now; other than that the gameplay seems to be the same.
After completing you first game there are new games available: Assignment Ada, The Mercenaries and Separate Ways (except for the Gamecube version). For the regular game, you can now play in Normal mode as before, or in Professional mode.