The chronocide's a prick, he only cares about destroying time he has no respect for his employees :(
Yeah the progress bar at the top is how many tiles you have yet to progress forward to reach the boss (starting at 100 when the boss spawns), congrats on going so far ! The 4th stage is the last and hardest one, the boss throws spells or enemies at you for every move you make at that point on top of having all of your spells locked out :)