The phrase "to prosecute the perpetrators" means to take legal action against the people who are responsible for committing a crime or wrongdoing. It involves bringing them to court and holding them accountable for their actions. Full definition
So, these same generals who have decided that Mubarak must be tried for his crimes are also prosecuting the perpetrators of the revolt against Mubarak: they are sending to goal those ordinary Egyptian citizens who have taken peacefully to the streets to register their protest against malign dictatorship. (blog.politics.ox.ac.uk)
During that time, he helped prosecute perpetrators of the 1993 World Trade Center bombing. (politico.com)
National governments with civil society and other development partners must do more to protect children and prosecute perpetrators if quality, inclusive education for all is to be achieved.» (globaleducationmagazine.com)