Destroy the third tower
As you may have surmised, the third tower is definitely going to be the most difficult one to access. Its nestled in the hills above an enemy base, which is itself packed with mercenaries.
Your first job is to just land the boat near the pier on the southern side of the island. You can find a boat by walking down the stairs near the destroyed second tower, so take it across the water and get out. Unfortunately, from here on in, youre reduced to simple gruntwork, of the attract-enemies-and-wait-for-them-to-approach variety. There are probably around two dozen mercs on this island, all told, a couple of whom have apparently had bionic eyes implanted, as theyll spot you from, quite literally, a mile away.
As you walk up the road from the pier and pass through the three rocks that block it off, get ready to hit the dirt as soon as your tension music queues up. The three soldiers who are most likely to spot you are in the three sniper towers in the base to your north; one possesses a sniper rifle, one a rocket launcher, and the third a regular AG36. A fourth owl-eyed bastard is manning a minigun near the rocket launchers tower. If you still have your sniper rifle, equip it and start dishing out justice, a dish thats best served cold! Or something like that.
After the primary threats have been dealt with, youll probably hear a 4WD coming your way from the rear of the island. Hunker down near the road leading up from the pier and shoot out anyone who gets off the truck, then claim it for your own. If you still have mercenaries that are hunting you down, you might just want to wait somewhere for them to come within view, before issuing headshots for the house.
When youve foisted a modicum of order onto the island, you can proceed into the merc base and loot the buildings and towers. When youre ready to move on, knock out the third tower in the hills above.
Go and destroy the freighter!
Just in case all this running around wasnt enough, youre given a new surprise task; now you have to assault and destroy a freighter in a nearby harbor. From the tower, grab the 4WD and gun it towards the western end of the island. When you spot a couple of mercs in the road, gun them down and get out of the truck. You should be able to spot the freighter from this position, or a little bit further west, but you definitely dont want to let the snipers aboard spot you just yet. If you grabbed the sniper rifle from the mercenary base, or already had one in your possession, you can use it to take down the boats defenders from here; just lie prone behind the large rock and strafe left or right until you spot a target. There should be one sniper and two rocket launcher foes, so check the ship with your binocs to make sure the exterior is clear before taking the nearby boat and climbing up the chains on either side of the ship. There will still be a few mercs left on board, so be cautious as you make your way up to the bridge.
After grabbing the explosives, refill your health and armor and grab a full load of rocket ammo. Youll find the fuel cell at the rear of the ship, so plant the explosives there. The explosives detonate after 25 seconds, which will cripple the ship and slowly sink it; Col. Crow flies in to try and take you out in the meantime.
Since Crows on a helicopter, youre going to be at a marked disadvantage if you actually stay on the ship; his minigun will cut you to pieces as soon as the water rises enough to force you to swim, and even before that occurs, youll have a tough time dodging his fire without getting hit. The thing is, although Jack seems to think the front of the ship is the safest spot to survive the explosion, youre actually better off jumping overboard as soon as you plant your explosives, and swimming towards shore. You may take a bit of damage from the explosion, since you wont be able to move as quickly, but you should survive, at any rate.
When youre ashore, pick a sizable palm tree and stand next to it as Crow flies in. Crows attack heli moves in the same fashion as the previous choppers youve seen; itll swoop around until its close, and then itll start strafing around your position, so that Crow can fire on you from the minigunners position. If you picked a big enough palm tree, though, you should be able to simply hide behind the trunk whenever Crow fires, thus rendering you able to survive the fight without taking any damage at all, in most cases. All you need to do is sit behind the tree, moving so that Crow is on the opposite side, and occasionally pop out and fire a rocket at the helicopter. Youll obviously want to do this when the chopper is moving slowly; you only have a maximum of 14 rocket rounds, and the helicopter can take nine or so hits before it flies off and explodes. If you run out of rockets, switch over to your OICW and use its HE rounds to finish the helicopter off.
Although Crow survives the encounter, the destruction of the chopper signals the end of this long level.