Characters must fulfill certain responsibilities throughout the course of Stupid Mario Brothers.
Also, it is prophetically his responsibility as one of the Chosen Ones to fight "someone else" while Wario fought the Darkness. Luigi becomes Mr. L and Mario battles him with his new-found full potential to bring his brother back to his senses.
Wario was responsible for battling the Darkness as the second Chosen One. He did so, though he had to say the counter curse to defeat him again. The Darkness would later reveal the uselessness of the curse as he was able to come back anyway by using the group's powers.
Waluigi's responsibility was to protect Wario by helping Mario and Luigi convince him to join their side. He trained them and then faced Wario. Later, he gave his brother the counter curse he originally forgot about.