In 1998, Rugby Canada and the provincial unions agreed to form the Rugby Canada Super League. Fourteen unions and sub-unions were invited to compete in the new semi-professional league. However, the Niagara Rugby Union (along with the Toronto Rugby Union and the Eastern Ontario Rugby Union) decided not to participate. Both Toronto and Eastern Ontario joined the league the following year, leaving Niagara as the only invited union not to join.
The Niagara Rugby Union finally decided to field a team in time for the 2004 RCSL season. The new club was named the Niagara Thunder.