For many years, Hamilton had an unstable presence in the ORFU, with various teams folding and being renamed, as well as a more established IRFU team, the Hamilton Tigers. World War II proved to be disruptive to both leagues' operations. In 1940, as part of a wave of hastily-assembled teams brought together to fill the void of the ORFU teams that had suspended operations, the ORFU returned to Hamilton with a teaminformally named after the Hamilton Alerts, a short-lived and long-dormant team notable for winning the 1912 Grey Cup. In 1941, the Tigers suspended operations due to the war, and the IRFU as a whole would do so from 1942 and 1944, leaving many talented players to join teams in the ORFU as well as a void in Hamilton football. Hamilton's ORFU franchise requested to use the Tigers name and colours but were rebuffed, opting to take on the name Hamilton Wildcats and use colours of red and white. The Wildcats' usage of numerous Tigers alumni led the Wildcats to a very successful three years in which they posted a 19–6–1 record with two appearances in the Grey Cupchampionship game with one win coming in 1943. In the 1943 and 1944 seasons, the team is officially recognized as the Hamilton Flying Wildcats due to the RCAF personnel playing on the team. Consequently, the team that won the 31st Grey Cup is recorded as the Hamilton Flying Wildcats. After the war ended, the IRFU resumed operations and players that had played for the Tigers were returned to their club. The Wildcats dropped the "flying" from their nickname since the RCAF personnel no longer played for them. After a difficult season in 1945, which saw the club miss the playoffs, the Wildcats claimed back-to-back regular season first-place finishes in 1946 and 1947, but lost in the ORFU finals both years.
Interprovincial Rugby Football Union and merger
Due to monetary disputes that the Hamilton Tigers were having with the IRFU, the Tigers transferred to the ORFU, with the Wildcats switching to the IRFU on April 9, 1948. The switch proved to be difficult for the team, who went from first in the ORFU to dead last in the IRFU, with only one win in their two seasons in that league. Both teams were struggling to compete for fan support and the financial repercussions started to mount. As a result, local prominent citizens including Mr. Ralph W. Cooper, Mr. F.M. Gibson, Mr. C.C. Lawson and Mr. Sam Manson decided that the two clubs should amalgamate and operate as one entity. As such, the Hamilton Tiger-Cats football club began play in 1950 in the IRFU as the singular representative of the city of Hamilton.