Let me break down what happens when you keep going against the emperor, since timing really matters here. During early encounters watch for their subtle reactions - if you destroy the tadpole or reject their guidance, they'll shift from cooperative to cold pretty quickly. Standing against them locks you out of some powerful illithid abilities like fly and psionic dominance, which become crucial during later fights. The real tactical impact comes in act 3, right before the netherbrain sequence, where opposing the emperor forces an additional boss encounter instead of having them as an ally.

For optimal positioning during the final stretch, maintaining at least neutral standing until after reaching the netherbrain chamber gives you more strategic options. The emperor's attack patterns become more aggressive if you freed orpheus earlier, adding mind flayer reinforcements to the fight that you'll need to manage carefully. Companion positioning matters too - keeping gale and shadowheart close drops their approval if you're hostile, while lae'zel actually prefers when you side against the emperor. Your romance options with them get completely locked if you show defiance before specific story triggers in act 2.

Just remember, the consequences adjust difficulty and story flow rather than breaking progression. You'll still have access to all major endings, but the path there requires different tactical approaches depending on your earlier choices.