Rupture Wave

After Kane purposefully destroyed his generator, causing his starship to crash near South City, it released a "rupture wave", which supposedly ruptured/disturbed the DNA of many people and gave them special abilities, though it killed a few people. However, it was eventually revealed that the wave infected people with nanites, giving them their abilities.

Trivia

 * Although most villains appearing after Season 1 were hit by this wave, giving them their powers, it is not the first time people were given powers, as a few villains beforehand were in some accident which gave them superhuman abilities.