Late to the party here, but yeah that was my take as well. As the inner simulation was about to burn planet express down, the professor made a comment about how catastrophic it would be given all the "doomsday" devices he has. I inferred that to mean that if all those doomsday devices went off, the outer simulation would be unable to simulate it, revealing that the "main" simulation was a simulation in itself; so outer bender came to the "main" simulation with the intention of stopping that from happening.