He started to search for the diaries of Destiny around the same time as Storm's team of X-Men. During one of the team's earliest missions, Vargas surprised them with his sword skills by murdering Psylocke and critically wounding both Rogue and Beast. Disappearing with one of the diaries, Vargas foresaw himself being killed by Rogue, and despite his belief in the prophecies of Destiny, he attempted to stop this eventuality from happening. During the invasion of Madripoor, Vargas returned in the midst of the battle, spearing both Rogue and Gambit with his blade before escaping.
Returning to the city shortly after the battle to recover his sword, Vargas was surprised by Rogue, who was dressed in Psylocke's costume. After a lengthy battle Rogue stood above him with his sword, poised to strike a killing blow. Rogue may have 'fulfilled her destiny' by finishing Vargas off with his own weapon, but this is not shown.
Not much was known of Vargas while he lived, and since his supposed death at the hands of Rogue, he has become something of an even larger mystery. It has never been stated if Rogue actually killed Vargas, but implies that Rogue actually let him live in order to defy the diaries.
In X-Men (vol. 2) #202 it was revealed that Rogue had in fact chosen to spare his life, as it was claimed that Vargas was killed by the Marauders later on instead, due to the fact he had knowledge of the future after reading one of Destiny's diaries. The Marauders have lately been slaying all characters who are able to "see" into the future.
According to Chris Claremont: "Basically, the notion behind Vargas is that nature, abhoring a vacuum and perceiving one in the appearance of mass numbers of super-powered mutants, is attempting to redress the imbalance by jump-starting Humanity to a level where they can compete with mutants and super-beings on relatively equal terms."
Vargas seems to the first known representative of the primary humanity's response and potential to cope with the growing number of genetically different humans which threatens the future of the conventional humans.