Complex sentence: Sections of the tunnel, as well as the Cortlandt Street station, which was directly underneath the Twin Towers, were severely damaged by the collapse and had to be rebuilt, requiring suspension of service on that line south of Chambers Street.
Split into simpler sentences: Sections of the tunnel, as well as the Cortlandt Street station, which was directly underneath the Twin Towers, were severely damaged. Rebuilding required the suspension of service on that line south of Chambers Street.