For one of my personal most "wrong" episodes, is For the Uniform in Deep Space 9. To summarize
Sisko: I'm pissed! Eddington embarrassed me!
Dax: Oh my, Eddington just announced he has WMDs, and he threatened to use them on Cardassian colonies!
Sisko: WHAT? We better go after him!
*Some time passes*
Eddington: See Captain, just leave the Marquis alone, you're coming after me because I hurt your feelings. You're being like this antagonist in this book I enjoy.
Sisko: Oh, I know how to catch Eddington. I'll be the bad guy! Worf! Prepare a WMD for a Maquis colony!
Whole Crew: Eh, Captain....aren't you a bit out of con-
Sisko: Shut up and fire!
*Maquis colony is just gassed by a Starfleet officer*
Eddington: Jeez, I'm supposed to be the terrorist Maquis, you're the Starfleet officer, who's supposed to uphold the morals of the Federation. Didn't you just have Worf almost extradited to the Klingons after he was accused of blowing up a civilian ship during the heat of battle?
Worf: Yeah, something about losing battles and even our lives to keep innocent civilian lives out of harm, rig-
Sisko: The continuity levels for this episode have been reached by having a Maquis plot! Now surrender, or we'll keep doing this.
Eddington: Sigh, fine. You win.
*Back on DS9*
Dax: You didn't get approval for your whole gassing a colony plan, did you?
Sisko: I knew I forgot something...Psh, they're only Maquis.