Baldur's Gate II: Shadows of Amn has a large central, nonlinear plotline which is broken down into 7-8 chapters, with lots of subquests and small adventures thrown in for variety. The number of item recovery type quests have been greatly diminished and there will be more class- and alignment-specific quests. Completing quests will have greater consequences and recognition as well. The story unfolds thorough dialog which has been made much more complex. Although the amount of dialog has also increased, it is presented more concisely, increasing the speed and your ability to interject. In multiplayer, most dialog does not pause the game and require everyone to watch; only the most significant information will do so.
You are a product of the Time of Troubles, a cataclysmic period in the Forgotten Realms when the gods were made flesh and forced to walk the earth among their followers. One such deity foresaw both the event and his inevitable downfall because of it, and left a score of mortal progeny across the land, intended to fuel his rebirth. Your fate is intertwined with that of this god, this Bhaal, Lord of Murder.
In Baldur's Gate during the year 1368 DR (12 years after the Time of Troubles), the Sword Coast was destabilized when a strange plague caused a shortage of iron, the lifeblood of a medieval-esque society. You brought the area back from the brink of war, and thwarted the plans of that madman, Sarevok, that sought to build a rule with paranoia and death.
In Baldur's Gate II: Shadows of Amn, early the next year (1369 DR), you face an uncertain future, with a lineage that tempts the unscrupulous to use you and the ignorant to fear you. You will face a foe that views you as no more than chattel, that toys with you at every turn; a villain whose goals go beyond a quest for power, and who threatens to use a lost companion as a tool for destruction unparalleled. The choices to be made will not be easy, and you may have to align with the lesser of evils, when all evils cannot help but seem equal. In the end you will have mourned lost loves, celebrated new ones, and had adventures that profoundly shaped the Realms.
You begin the game imprisoned in Athkatla, the capital city of Amn. Unaware who your captors are, you are bouyed by seeing your friends Imoen, Jaheira and Minsc (with Boo) nearby. You need to free them and then figure out who captured you, as it isn't the law. As a prisoner, your equipment has obviously been taken away from you. Where it is, you have no idea [those starting new characters will have no equipment to find]. You will be able to find some of your equipment as your leave the initial areas while some other possessions will be used to improve items you find along the way. For instance, a new character might find a Long Sword +1, while your character will find his trusty Long Sword +2. From your imported character or saved game, BG2 would scan for items that are included and those items are moved to their appropriate areas. Then the character's (all characters in the case of a MP game) inventory is deleted. If you import all the characters in a multiplayer game, they will all be locked up and lack their equipment, as in the single player game.
Athkatla is a very large city, much larger than Baldur's Gate. The areas making up the city are much more packed than in the original game with very few of the houses being empty. The city has a large halfling population and some elves.
To teach new players how the game works, a detailed tutorial session will be selectable that is not part of the storyline. The tutorial will include everything from party tactics and movement, to spell casting and item use. This will serve the same purpose as your initial Candlekeep adventurers in Baldur's Gate.
The story takes place in Amn, south of the Baldur's Gate region of the Sword Coast. You will also adventure in the Elven forests of Tethir, underwater cities of the Sahuagin, the Cloudpeak Mountains, at the pirate isles and city, the Astral plane, cities of the Underdark including one of the Drow, and the Abyss (Hell).
There is one plot involving seafaring and ships.