He calls him 'Sir'.
CLU knows that he's the only program that he's ever heard of to call their User 'Sir'. Typically, a program uses the authorized designation of their User. But somehow, it seems right.
Maybe it's because, as a hacking program, he does his best to ignore any other authority on the system. He doesn't call any of the military or security programs 'sir'. Not even as a snide bit of sarcasm. Why bother to show them that much respect, when he will be breaking all of their rules and regulations later?
Honestly, he doesn't even say it to the Tower guardians.
But he just can't bring himself to address his User as nothing more than $Flynn. After all, CLU IS the best hacking program to ever hit the Grid…his User told him so. And if CLU is the best there is; his User must be far more that simply $Flynn.
He will do whatever he is directed, break every rule that blocks him, and go into any restricted area without flinching. And he will do it all for his User; because his User has given him everything. And while he has absolute faith in his User, his User has told CLU that he has faith in him.
Thank you, Sir.
A/N-I had no intentions of ever writing/posting this...but that stubborn little hacking program simply REFUSES to quit...