Main Quest: The Palace of Machines
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"We defeated the Professor's mechanical general and destroyed an army. So what have you got planned for the rest of the day?"

After protecting the Secret Lair from Professor Fulmigati's minions, when you talk to Vlados next, he'll tell you that Fulmigati has fled to the Palace of Machines -- where he plans to activate his Mechanical Colossus, also known as the Doomsday Automaton. So you'll need to track him down before he can make his machine operational.

To reach the Palace of the Machines, you'll first need to make your way through the Old Town, which is the largest map area in the game. It will take you while to explore the area, and eventually you'll realize that all of the streets leading to the Palace of Machines have been blocked by force walls. At that point you'll decide to return to the Secret Lair so you can see if Borislav Tveter has a way to get around them. He won't, but he'll tell you that the "true genius" who invented them can be found in the Industrial Port.

The Industrial Port will be a little different in Chapter 3 than it was in Chapter 2, and it will be reset with new enemies and treasure chests. On the upper, eastern part of the port you'll find an entrance to the inventor's Secret Laboratory. Inside, you'll have to run a gauntlet of sorts (which will be much easier if you have ranged attacks), but you'll find the inventor on the lower side of the area, past an elevator.

When you talk to the inventor, he won't want to deal with you, and you'll have three ways to respond: you can use diplomacy, you can bribe him with 10,000 gp, or you can threaten him. For the two non-financial solutions you'll have to fight the automated turrets in the room, but regardless, the inventor will subsequently tell you that there isn't any way to disable the force walls. However, he'll add that there is a way to go around them, and he'll create a portal for you, which will take you to the Pocket Realm.

From this point you'll just have one way to go. The Pocket Realm will lead to the Gables, and the Gables will lead to Rooftop Mayhem. When you reach Rooftop Mayhem, you'll complete the quest and earn a random "yellow" item plus 1000 xp.