By the late 1990s, the seven units saw continued use around Manchester. They also saw some use on longer distance services, with one booked daily Manchester Piccadilly-Birmingham International service and return. On occasion, units were used on NWT's Manchester-London Euston service, deputising for a non-available Class 322 unit. At one point, it was planned to use the units on a new - stopping service, but this did not happen. However, the end was in sight, because as part of their franchise commitment, FNW had to replace their slam-door rolling stock, including the Class 309 units. New Class 175 diesel multiple units were introduced in 2000, and FNW discontinued its Manchester-Euston service. This meant that the "Clacton Express" units were surplus to requirements. As a farewell gesture, three units were used on a final railtour from Manchester to their old haunt of via London Liverpool Street. Following this tour, all seven units were withdrawn in late 2000, and sent for storage at MoD Pig's Bay near Shoeburyness. Two of the units later saw further use in departmental service, whilst the remaining five were scrapped in 2004.