With the service now being more reliable, passenger numbers continued to grow and by 2000 the busiest trains had got to the point where they were breaking Passengers In Excess of Capacity restrictions. As a temporary measure Great Eastern contracted First Essex Bus to run a non stop service in each direction during weekdays starting on 25th September 2000.

Early 2001 and First Great Eastern promised they'd be able to solve the overcrowding problems at the May 2001 timetable change, they'd located a spare 2-car Class 150 unit from Arriva Trains Northern (150245) which would be transferred to Anglia Railways, who would then lend a 150 daily to Great Eastern.
Class 150s took over the branch weekday service on 21st May 2001, with 150255 doing the honors, for this day steps were provided on the platform at Marks Tey to line up with the doors and bridge the gap between the train and the platform edge, the supplementary bus service was withdrawn from this date.

Also in 2001 with the help of the SRA's Rail Passenger Partnership, First Great Eastern was able to secure a sum of money in the region of £80,000 to operate a Sunday service up until the end of their franchise. The Winter Sunday services started on the timetable change in 2002 - plugging a gap in the timetable which had existed for many years.

Summer 2002 saw the Gainsborough Line enter the Essex and South Suffolk Community Rail Partnership, this was already in operation for the Harwich, Southminster, Clacton and Walton Lines, and with the addition of Suffolk County Council as a main partner, the Sudbury line was able to join, which would give the local people a change to form an Action Group to help promote their line.

In late 2002, the SRA announced that as of 1st April 2004 the Great Eastern and Anglia franchises would be merged to form a Greater Anglia franchise, and in December 2003 after a bitter struggle, which saw First Group excluded from bidding, subsequent court action, then finally First purchasing GB Railways (parent company of Anglia Railways), National Express Group were announced as the winner.

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