The Elder Brain is the main cause of the protagonists' adventures, so the entire plot of Baldur's Gate 3 revolves around it. The first encounter with it occurs in Act 2, where players learn who is behind the Illithid tadpoles plague and how they control the Elder Brain. However, the game doesn't give a chance to fight it unless Gail blows up his orb, which is clearly not the best solution. The main encounter with the Elder Brain will take place in Act 3, but you may need help finding and confronting it in Baldur’s Gate 3.