I ran this by a friend of mine and he thought it was a pretty solid plan so I thought I'd run it past you guys and see what you think.
Clearly I got this idea from Justice League: Doom, but I realized that many of the plans are flawed when Savage lays them out. For example the plan to take out the Flash is dependant on his want to save people (which wouldn't be an option if he were to turn evil), and the plan for Wonder Woman was somewhat nonsense in my opinion, and lastly, but most importantly, Martian Manhunter's plan only took him out the game for as long as it took for the substance to get used up in his body.
So I should clarify some things before I begin. When I say "Justice League" I am only referring to the Big 5 JL heroes (other than Batman) that played a major role in the JL: Doom movie. Which are Superman, Wonder Woman, Flash, Green Lantern, and Martian Manhunter (Cyborg is relatively easy for Batman to take out in under the circumstances of the scenario that I'll lay out in a moment, so I'm not including him.) And lastly there is one member that I just cannot kill without magic or BFR.
This situation, unlike JL: Doom, is if I were to become Batman with his intellect and resources but be evil and want to defeat these members of the Justice League. The other members of the Justice League would believe me to be the Batman they know and trust. I have the amount of time I require to prepare and carry out this plan. Under this logic I feel that I could use an electromagnet or an EMP to kill Cyborg easy enough so he is not a part of my master plan.
So without further ado, I present my plan to defeat the Justice League.
Step 1) Sneak up behind the Flash and break his legs so he can't run away but is still alive. Before I kill him I make sure he lets out a cry for help (I kill him in any way you could kill a regular person I suppose).
Step 2) As he calls for help I throw up a piece of kryptonite so when Superman super speeds into the room to save his friend he collapses from the radiation. And while Superman is powerless I kill him. (I would make sure to stab him through the head and the heart and then maybe behead him to be extra sure his "healing coma" wont be a factor.)
Step 3) This is where I would want to take out Martian Manhunter because of his telepathy, however I can't think of a way to kill him assuming fire doesn't hurt him and he's only afraid of it... So I guess I send him to the Negative Zone.
Step 4) Then I would take out Green Lantern. Similarly to JL: Doom, I would use scarecrow fear gas to weaken Green Lantern, and then while he is trying to gain his bearings I'd cut off his ring finger. And then kill him in any way you could kill a regular human being.
Step 5) Lastly we have Wonder Woman. In all fairness I'm not sure if this one works perfectly, but feel free to let me know if this doesn't line up. Using a giant electromagnet I keep Diana in place because of her bracelets. After making sure she is subdued I take an object that can become intangible or tangible (something I'm fairly certain Batman can create although I couldn't find a scan of anything resembling this) and I would turn the object intangible, put it into her head then make it solid again killing her.
And thats how I'd kill the Justice League. What'd you think? The one major hole I know exists is that I'm leaving Manhunter in the Negative Zone plotting his escape.