"I will not make any deals with you. I have resigned. I will not be pushed, filed, stamped, indexed, briefed, debriefed or numbered! My life is my own."
Number Six's Paranoia Gambit in "Hammer into Anvil": convincing Number Two that he was planted in the Village to test Two's loyalty, and then to report himself for disloyalty because he tried to interfere. Given that this episode is usually seen as one of the last in the series, it's a clear sign that to the Village, Number 6 is not just frustrating anymore, he is getting dangerous.
In the episode "A, B, and C": Number Six is hooked up to a machine that projects his dreams onto a screen, then injected with a drug that will allow Number Two to control his dreams. Six (during the day) figures out the plot, replaces the drugs with water, then directs his own dreams that night. When he dreams he is walking into the room Number Two is standing in, Two turns and looks at the door to see if Six is actually coming into the room. Even though Six is lying right in front of him.
A scene in the episode "Checkmate" where Number 2 is meditating in front of a piece of plywood. He picks up a ringing phone, receives urgent news of the lighthouse being attacked, calmly hangs up— then, letting out all his rage at once, karate-chops the plywood in half.
Number Six (along with the Butler, Number Two (McKern), and Number 48) shooting his way out of the Village in Fall Out.
In "A Change of Mind," Six is attacked by two hoodlums out of nowhere, which gets him branded "unmutual" and set up for a lobotomy. Of course, it's all just a scam that the current Number Two is running, but the two thugs don't know that, and when they approach Six to beat him up again, he snaps out of it and kicks both their asses.
The Village has switched Number Six's mind with The Colonel's, wiped it, and sent him out to find the one man who could reverse it. When they have all three men back, the scientist leaves the Village in the Colonel's body, Number Six is back to normal, and the Colonel dies from a heart attack.