Ok, i only got to the part where I get on the boat to meet this dude and it blows up.. Is that the real ending? or is there more??

Haha, yep, game over. That is the end of the story mode. I wish you could save afterwards and then continue from there in the city. I was upset at first, but I made a save before the last mission or two. You still get the achievement credit of beating the story, even by reverting to an old save to play side activites and such.

I suppose you're just dead. Boat goes kablooie and you do, too.

I've also finished the game, and i did all activities. My percentage is now 96%, and i suppose the last 4% are supposed to come from that last "mission".
Could anybody here verify that after doing all activities the maximum percentage to get is 96% ?

PS. i advise everybody to play all activities first before you start doing the missions. That way you have a asskicking character with lots of free guns and infinite running etc before you even start doing the missions.
So you'll have much more fun during the missions, and you won't have to let any enemies live due to low health, because your character will be strong as a beast