Most of the patent covers ways of dealing with the theft of a phone, but broadly, it addresses "hacking, jailbreaking, unlocking, or removal of a SIM card."
Mashable explains how Apple could use the technology:
Obviously, Apple's not going to deploy such a drastic measure wily-nilly, but it's certainly worth keeping in mind that they might have such abilities stashed away in Cupertino.
[T]he patent also covers methods for identifying devices that have been hacked, jailbroken, unlocked or had their SIM cards removed, such as monitoring sudden increases in memory usage that could "indicate that a hacking program is being run and that an unauthorized user may be using the electronic device." Theoretically, Apple could then wipe personal data from these devices and then alert AT&T to "shutdown any telephone service to the electronic device, shutdown the electronic device itself, or otherwise suitably extract the functions of the electronic device."
In other words, the system described in the patent allow Apple to effectively kill jailbroken devices under the guise of protecting customers from theft, since it may not be able to determine whether a device has been stolen or if it is being willingly jailbroken by users.