While the club won the Grey Cup in 1912, but not without controversy. The Alerts were suspended by the Ontario Rugby Football Union on November 23, 1912, one week before the Grey Cup game, after questioning the Union's authority. After the Toronto Rowing and Athletic Club protested a questionable penalty call in a Hamilton Alert's victory, the ORFU ordered the Alerts to replay the game on November 23. The Alerts lost the rematch 39–7, mainly because they used backups while the main squad played the Hamilton Tigers in a regularly scheduled match – which the Alerts won 12–8. The Alerts proceeded to defeat the Toronto Argonauts in the Grey Cup the following week.
The Alerts tried to rejoin the ORFU with a formal request on September 6, 1913, but were denied reinstatement. This, along with the previous season's indiscretion, led many players to join the Hamilton Tigers of the Interprovincial Rugby Football Union in time for the 1913 season. What was left of the Alerts operated separately from any union for several years until they disbanded altogether.
In 1940 several ORFU teams disbanded during the war, and several more were quickly thrown together to ensure a season was played. The team from Hamilton was nicknamed the "Alerts" by the press, but was not a descendant or continuation of the original team: they won 1 of 5 games in 1940.