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When you arrive at the Throne of Bhaal, Melissan will be in the process of absorbing Bhaal's essence (#1). But when she spots you, she'll jump out of the essence chamber and attack you (#2). This will start a long sequence of battles where you'll have to repeatedly fight Melissan and then take essence away from her.
Each time you fight Melissan (#2), she'll start out at full health. She'll cast some spells (like Earthquake) and summon some creatures (like balors, bone fiends, death tyrants, glabrezu, mariliths, and slayer shadows), but mostly she'll just whack you with her spear. When you do enough damage to Melissan, she'll retreat back into the essence chamber (#1), and any summoned creatures with her will disappear. So for the quickest battles, you should focus on Melissan and ignore her summoned creatures as much as possible.
When Melissan retreats, all combat will end, which means you'll be able to save. But you won't be able to rest at any time during the encounter, so try to parcel out your spells and high level abilities for the seven battles that you'll have to fight (four against Melissan and three against her guardians). Also, be sure to take advantage of the intermissions between battles to heal up your party -- and perhaps place some traps at the place where Melissan will always appear (#2).
To continue fighting Melissan, you'll need to cut her off from Bhaal's essence by closing the three essence pools (#3-5). You'll encounter some guardians at each pool, but you're not required to kill them all. Defeating the boss creature at a pool -- the prince of air, the prince of ice, or the fallen solar -- will allow you to interact with the pool and close it. Of course, as soon as you close a pool, Melissan will exit the essence chamber, and you'll get summoned back to her for another round od combat. So you'll have to choose between a quicker fight at the pools and then immediately fighting Melissan again, or a longer fight but then having some time to prepare for Melissan. You'll have to fight Melissan each time you close a pool, plus when you arrive, meaning you'll have to fight her four times.
When you defeat Melissan for the fourth and final time, the Solar from the
will teleport in, and she'll declare you the victor. You'll then have to choose whether you want to become a god or not. This is just a role-playing decision, and it will only affect your ending story. Congratulations for completing Baldur's Gate II!
Note: If you have a lot of trouble winning seven fights without resting, then one trick you can try is to memorize the Wish spell (which you can purchase from Lazarus Librarus in Amkethran). With 18 Wisdom (which you can achieve by quaffing a Potion of Insight), there's a 20% chance that the Wish spell will allow you to rest.
1 - Essence Chamber
2 - Melissan Battles
3 - Essence Pool
At this essence pool, you'll encounter two greater air elementals, two vampiric wraiths, and Yan-C-Bin, the Prince of Air.
4 - Essence Pool
At this essence pool, you'll encounter two blizzard trolls, two frost salamanders, and Cryonax, the Prince of Ice.
5 - Essence Pool
At this essence pool, you'll encounter an alu-fiend, two mariliths, a succubus, and a fallen solar. This essence pool battle is much tougher than the others, so be prepared.