That is a good question. How do you fake a mass prison break? Some ideas:
1.) Illusions would be one method.
2.) Contacting the prison and AGEIS, then rigging and elaborate mass impersonation scheme is another; wherein AGEIS agents and/or guards take the place of the various criminals.
3.) Again, work with the prison officials and AGEIS, but this time have them implant some kind of delayed knock out pill in prisoners. So when they get out, once the Grue are on their way the capulse/device/whatever can be activated and puts out the villains so they can be rounded up. Not even sure if that kind of gear is avaible though.
4.) Once more, contact AGEIS and prison officials. However, this time around its to see if they can recruit the villains to our cause. Tell the prisoners about the Grue invasion, and offer them some kind of deal. If they help fight the Grue and Omega they get time off their sentances or the like.
THough the more people involved, the more likely a Grue infiltrator would find out. So those last three probably aren't that great.