The newly formed club had struggles in the Conference and were relegated to the Isthmian Premier League in the 1995/6 season. An FA Trophy final appearance against Woking was the highlight of the 1996/7 season, Dagenham eventually losing 1-0 when down to ten men.
A period of progression and stability kicked in and Dagenham finished fourth, fourth and third in consecutive years before winning promotion back to the Conference with 101 points, only dropping two points at home. Garry Hill lead their charge into the Conference they came incredibly close to promotion and beating a Premiership team.
They had beaten Lincoln 1-0 in the second round of the FA Cup and they were four minutes away from defeating Charlton Athletic at the Valley. They would eventually lose the replay 1-0.
2001/2 was one of the most controversial seasons in the Conference. Dagenham and Boston were headbutting each other for the title all season long. However, Boston eventually finished top and won promotion into the Football League. However, it emerged in the following weeks that Boston had given illegal payments to their players and a points deduction was carried onto the next season. If it had been taken off the 2001/2 season total then Dagenham would have been promoted instead.
2002/3 was most remembered as an eleven match winning run broke a Conference record. They finished 4th and qualified for the first ever Conference Playoffs. A penalty shoot out victory over Morecambe was rewarded with a final appearance against Doncaster Rovers. The teams went into extra-time level, but a late Francis Tierney golden-goal ended Dagenham's hopes again.
The 2002/3 was a bit of an anti-climax. The Daggers were amongst the favourites for promotion but failed to live up to exceptions and broke another Conference record along the way. A Sky Sports covered game against Hereford United resulted in the Daggers suffering a humiliating 9-0 defeat, which to this day is still the highest win/biggest defeat in that division.
Garry Hill left and John Still took over, finishing a respectable 10th position in his first season as manager. The 2005/6 season was another midtable finish but the 2006/7 season was memorable for the Daggers. A season long battle with Oxford United at the top of the table eventually saw Dagenham pull ahead and a 2-1 win over Aldershot meant that Dagenham won promotion to the Football League for the first time in their history. In an almost ironic twist, they replaced Boston United.
Dagenham's first season in the Football League was one of struggle and despite the arrogant claims of their fans, they didn't take the division by storm. Infact, they came within four days of being relegated back to the Conference at the first attempt.
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