Are you referring to authenticating with the Kabam servers? Or some other type of security check?
The game appears to work almost completely offline, sending fight data packets to Kabam after a fight is finished. The Coperius mod and the mod updated here for iOS will get you banned if used in the wrong areas of the game. Seems that Kabam only checks high-end content though. "Wrong" areas being the newest content, or anything Alliance-related.
Looking at the code for MCoC mod, he simply used functions already available in the game - probably for developer/QA testing. Options like turning off NPC attack, increasing base damage, etc. It's a unity game, and none of the code appears to be encrypted that I've looked at so far. At first glance, it looks like he created an in-game menu to turn some of these functions on or off, but didn't modify any other sections of the game.