This page of the guide to Baldur's Gate 3 has a summary of Baldur's Gate 2: Shadows of Amn.
NOTE! Here we summarize only the main plot of Baldur's Gate 2. A description of side quests would take up the entire book. And there's a lot going on in the main story. I mean a lot.
The adventure continues. Although you defeated another Bhaal's child and you brother, Sarevok, this has solved only one of the many problems. You have to deal with Lord of Murder's legacy - and the people who are interested in it. The second part of Baldur's Gate takes you to Amn, a fantasy land that differs greatly from the Sword Coast. The journey begins with a painful landing.
You start in a cell. All you hear is rusty iron, your own screams and someone's calm, cold voice. And the hissing of spells. Some magician is casting another spell on you to test "your potential". The torture session would probably have gone on if a golem hadn't taken the magician off the job and informed him about intruders. The magician leaves you in a cozy cage. Soon, Imoen appears - she helps you out and frees Minsc and Jaheira. You have to go through a few rooms full of monsters and horrors. The magician uses monsters and dwarves in work. He also imprisons other creatures such as genies and dryads and... undead former minions. One of the latter tells you the name of the torturer - Irenicus.
You reach the upper level of the prison by going through a portal hidden in the mage's chambers. There you are greeted by Yoshimo, a thief who has also been imprisoned in Irenicus' dungeon. Shortly after that, you find Khalid's remains. Jaheira falls into despair and swears revenge. You break through the next rooms, where Irenicus' servants fight the mysterious attackers. In one of the chambers, you discover that he was holding clones of an elven woman. The clone tried to attack you. After these traumatic events, you get to the surface.
There's even more trouble waiting for you outside. Irenicus fights and defeats the enemies. All you can hear are the sounds made by spells and screams of the dying. Imoen, in anger, attacks the enemy with sorcery. The illegal use of magical energy attracts the attention of Cowled Wizards. Our torturer defeats them, but the reinforcements are on their way. Irenicus has agreed to follow the "law enforcers" if they take your friend Imoen too. The confused Cowled Wizards take both mages to an unknown location. We are left among the rubble at a market in an unknown city with a headache, a lot of questions and a companion to save.
You starting by looking around. The people know very little about Imoen and Irenicus - you learn only that they were taken by the Cowled Wizards to make sure that no one is casting spells in Athkatla recklessly. Athkatla, the place you currently are, is the capital of Amn. You check out the circus, where you will solve a problem with a certain illusionist and perhaps meet a new companion. But it's just a side activity. After completing it, you move on...
Help comes unexpectedly. In the slums, you are attacked by a rogue, Gaelan Byle. He offers you support and a deeper insight into the situation. He can direct your party to the right people who know where Imoen is, but it will come at a price - 20,000 pieces of gold. That is a lot of money, but before the kidnapping you probably had gear that cost a lot more. There are many secrets to discover in Athkatla, many enemies to eliminate, people to save and money to make.
You have a lot of jobs to choose from. Do you want to get involved in the conflict between the local gangs? In fights between the nobles, or cultists? Hunt for a serial killer? Why don't you go out of town to take out the trolls who are harassing the fortress, solve the feud of the rebel druids, or explore one of the ancient temples? Along the way, you will meet those who will want to - or will have to - join you. Some will become friends (and will want to sell you some turnips...), a few of them will have an even stronger bond with you. Maybe. It won't be easy, but in the end you deliver a mountain of gold to Byle - at one point you got a discount because the competition, Gaelan's friends, made you an offer too. Either way, I assume you eventually went to Gaelan because the counter-proposal is... a different story.
When you hand over cash, the real game starts. You enter the world of those who pull the strings, rule the whole city, the underground, and every bandit (as well as politician and nobleman) must reckon with them. You join the Shadow Thieves, a powerful organization that rules Atkhatla. You meet one of the most important people of this group - Aran Linvail, the Shadow Master. He is the one who gives you the new tasks. After completing them, you will be able to go to the place where Imoen is held captive.
This means you get caught up in a gang war. Except your opponents aren't just bandits, they're vampires. You learn more about the group, weaken its influence, hunt down the Shadow Thieves' traitors, and finally make your way through the Athkatla Graveyard district to the guild's leader, a vampire called Bodhi. You defeat her undead servants, but the leader manages to escape. Nevertheless, the task was accomplished - the group broke up. Aran Linvail is pleased, and allows you to travel to Spellhold - a castle on an island where the cowled men are holding their "patients" and re-educating them. Your guide will be Saemon Havarian, a charming rogue. You will regret meeting him (guess who your captain would be if you supported Bodhi...). Either way, you go out to sea.
Sea waves, singing birds... You reached Brynnlaw, a port town on the island, without any problems. This is where you will find the Spellhold. There are several roads leading to the fortress. It is up to you to choose which path you want to follow. Know that if you have searched this place thoroughly, you could have stopped a pretty disgusting act, or at least be a nuisance the pirates hiding here. Or you can just act crazy until they send you back. It's not for me to judge. In any case, you break inside the Spellhold. You are greeted by a Cowled Wizard, who patiently shows you around the castle that looks like a luxurious prison. You can easily notice that something's not right. Other magically gifted patients behave as if they had their brains removed.
The same thing happened to Imoen. When you get to her cell, she barely recognizes you and acts like someone who went through lobotomy. Then your guide removes his hood and shows his face - it's Irenicus himself. You land in a glass tube. Your companion, Yoshimo, turns out to be a traitor who led to the Spellhold. You also recognize your good friend, Bodhi, who turns out to be Irenicus' sister. Everything stays in the family. The powerful magician performs a ritual on you... that rips your soul out. You resist, fall into a coma, face your demons and nature.
And then you wake up in the middle of a giant maze. However, you aren't alone - you have your companions and Imoen who regained consciousness. Bodhi is also here. Irenicus left you to become his sister's dinner. The vampire has a strange affection for you, which is why she's condemning you to a sadistic game of roaming these corridors. After that, she disappears. The bad news: she had previously taken a large chunk of Imoen's soul.
You break through the traps and fight the monstrosities waiting around the corners. There are plenty of opponents here. At some point, you will face your favorite bloodsucker. Although she initially gains the upper hand, you surprise her and yourself with your ability. You lose control and turn into a monster that throws Bodhi around like a rag doll. The vampire flees, struggling to hide her fear. As your battle frenzy passes, Imoen explains that you have most likely turned into the Slayer, one of Bhaal's avatars. This means that what's left of your soul is not looking good...
Armed with this knowledge, and with a new, disturbing power that you can't control, you break through to the end of the labyrinth. Saemon Havarian appears and suggests that you can get the support of the imprisoned mages in your battle with Irenicus. The prisoners, though seriously injured, agree with that. You face Irenicus. His magic almost destroys you, but the Slayer awakens again and helps you win. Surprised, Irenicus flees. Before you follow him, you must confront the wretched man you thought was a friend. For him, it's a matter of honour. Or rather an honorable, inevitable death. He wants to die at your hands, and he got it. You must now follow Irenicus. You can use the portal hidden in the Spellhold - or go with Saemon Havarian. As if you haven't got enough problems, you go with the smuggler...
Before moving out, Saemon hands you a silver blade without a hilt. The sea voyage is interrupted by an attack by Githyanki warriors, who are clearly looking for something (guess what). The Sahuagini (fish people) intervene and drag you to the undersea city. There, after freeing yourself, you resolve a dynastic conflict, then go further into the Underdark.
You think it's been tough so far? It is one of the more ghoulish places of Faerun (apart from the Athkatla slums). Welcome to the Underdark. Darkness is everywhere, and everything except maybe one good creature wants to kill you. Dark Elves, Mind Flayers, Umber Hulks, Duergars and every other monster you can think of. And a few you'd rather not think about. Troubles await around every corner.
The only friendly place is the camp of the Deep Gnomes, but they too have a problem. The said problem has large wings, teeth, and demonic powers. You kill a creature called Balor. As a token of their gratitude, the Gnomes show you and open the way to the dragon called Adalon. She knows how to get to Ust Natha, the Drows' city. This is where Irenicus and Bodhi went. The dragon is suffering from loss - the eggs she laid were stolen by the Dark Elves and hidden somewhere in Ust Natha. They did that so she won't make any move against the scheming Drows.
With the help of an illusion, you enter the city as a Drows delegation from another city, Ched Nasad. You are placed under the protection of the bitter Dark Elf Solaufein. You are given the task of recapturing the Matron Mother's daughter, which means fighting the Mind Flayers. After the battle with the enemies, you free the kidnapped Drow. As a reward Phaere, because that's her name, makes you part of increasingly more complicated intrigues. To maintain the cover, you follow orders that mainly involve killing political enemies (like Githyanki) and her former friends (Solaufein, whom you spare because you're not that committed to the role). She's using you to strengthen her position. You finally find out where Adalon's eggs are and why the Drows need them.
This is the moment when you have the opportunity to make a heist. The Matron wants to sacrifice the eggs to a demon. Phaere suggests that you place the fakes and give her the real ones. You follow her plan. As you head to the palace to hand Phaere the originals, Solaufein appears out of nowhere and offers you another copy of fake eggs. That's what you do. Matron and Pahere are killed, the demon gains nothing. You manage to get out of Ust Natha without blood on your hands. You also learn a bit about Irenicus' plans. The mage and Bodhi plan to take revenge on someone who took their souls from them earlier.
Adalon assists you in breaking through the Underdark and teleports you to the surface.
It's not like you're going to be given a rest. You are greeted by the elven blades. The Drows' distrustful surface cousins lead you to their commander, Elhan. There, it is revealed that you have a common problem - Irenicus, who attacked Suldanessellar, an Elf city hidden in the Tethyr forests. To make things worse, he blocked the access to them for anyone who was outside the borders. The lantern that opens the passage is owned by your good friend - Bodhi. With the support of the elves, you go in search of the vampire.
You're searching the woods where she may have been hiding, but you come across Drizzt Do'urden, a famous Dark Elf hero. If you have a friendly nature, he will join you. He wants to meet you at a specific place. You already know where Irenicus' sister is hiding. In the Cemetery District. The vampire strengthened with Imoen's soul (who also turns out to be Bhaal's child) decides to return to Athkatla and take control of it. You have enough reasons not to negotiate. You're looking for more allies, and if you've solved problems in a specific way earlier in the game, you'll receive help from the Shadow Thieves.
You were prepared for a challenge, but Bodhi has just made it even worse. If you had an affair with someone from the party, the vampire will kidnap that person. Shocked and angry, you walk through the cemetery and the catacombs, avoid the traps, and fight the undead. If you're lucky, you will be supported by those you have asked earlier. Finally, you reach the "queen's" chamber. Besides Bodhi's servants, you will also encounter your beloved or beloved - transformed into a vampire. You have to kill them too (and resurrect later). After that, you have to defeat Bodhi. By piercing her heart with a wooden stake. This will get rid of her once and for all. You thank your allies, Imoen gets her soul back, you take the artifact and go to perform a ritual to resurrect your beloved. And then you're getting ready for a final showdown with Irenicus. You're going back to Elhan.
You make your way through the forests of Tethyr (it is quite possible that you even meet a few friends from Baldur's Gate - friends who, of course, get you into temporary trouble). You finally reach the Suldanesselar gate. With the help of Rhynn Lanthorn, you open the passage and get right into a battle. Irenicus and his minions are wreaking havoc in the Elven city. Drows, demons and golems roam the streets.
You make your way through successive alleys and buildings hidden in tree branches, collecting some of the artifacts necessary to reach the mage - and the Tree of Life from which Jon wants to suck energy (by using the three parasites you kill in the meantime). The party encounters him and the elf queen, Ellesime. The mage used her to create clones. Now he's holding her captive with a spell. After the conversation, you learn that Irenicus, was taking revenge for his exile from Suldanesselar as well as for the loss of his soul and Elven nature. He also wants to take revenge for the love he felt for Ellesime. You can finally face him in battle. The sounds of magic, steel and battle cries become one in this deadly clash.
Irenicus finally falls to the ground, in disbelief of his own defeat. Just when you think it's over, the mage uses the rest of his strength and pulls you down... to hell. When you wake, there's no sign of Jon. Big gates and small passages await you. You explore the latter first. There's a trial at the end of each of these roads to test who you really are. This creates a risk that you will come out radically different. Not necessarily for the better. No one said we always have to triumph over our own demons. Either way, you can finally find Irenicus and face him one last time.
During this fight, he also manages to transform into a Slayer. The man is also accompanied by demons. Time for the final battle. If you lose here, you'll be lost forever. But you survived this fight. You took out Irenicus for good, and what's left of him will receive a punishment worse than death. And you... you get your soul back. Finally, you feel complete - complete enough for a descendant of a murderous deity with a beast hidden at the bottom of your of consciousness. You are brought to Suldanesselar, and for a moment you may think you will have some peace. Except you've actually just solved a private, temporary problem. The real storm is just coming.