Clarke wakes up in the City of Light after taking the chip in episode 3x16 "Perverse Instantiation: Part Two".
Mulder hides out of sight as the pursuer drives past in episode 11x01 "My Struggle III".
From episode 1x09 "Tigh Me Up, Tigh Me Down".
Source: BSG Season 1 Location Guide
Sam Flynn rides his bike up a ramp in the middle of downtown after escaping the cop.
The transport convoy drives into downtown.