Batman vs. Martian Manhunter
SETUP
Batman had some method of subdual prepared for every member of the JLA should the need have arisen to take them down.
At the time, Martian Manhunter was still vulnerable to fire, and the method Batman concocted for him was to have nanites attached to his skin that burst into flame upon contact with air, effectively turning him into a living torch.
Now that J'onn has overcome his previous fear of and vulnerability to fire, what would Batman come up with for his new contingency?
Essentially, this is Batman with six months of prep time vs. an unprepared (and potentially insane) Martian Manhunter.
Keep in mind that "unprepared" doesn't mean passive or foolish in this case. Assume Martian Manhunter is hostile to everyone, but not necessarily hunting for Batman specifically. When he does encounter Batman, he would approach him with full knowledge of what Batman is capable of, but he is unaware of whatever particular plan Batman has prepared.
RULES
1. Bringing in other members of the JLA is not an option.
2. Bringing any other beings into it is extremely unlikely, as they could introduce a level of unreliability that Batman would prefer not to deal with.
3. Technology
a) Any technology used must be constructed by Batman himself. No borrowing existing weapons from others. Secrecy is key.
b) Size/Portability is an issue. Weapons or machines should be able to be used or accessed under practically any circumstance and should not require the target to be standing on a big X in order for them to work.
c) Stupidly generic technology shouldn't be used. Examples are "an anti-martian ray", "a helmet that blocks all telepathy", or "something that prevents intangibility". You don't have to be a scientific expert (although it's certainly a plus if you are), but at least make an attempt to intelligently explain how and why something works.
d) No magic.
4. Unless absolutely necessary, excessively destructive forces are off limits. The idea is to protect the earth from the threat of Martian Manhunter gone bad, not take half of it out in the process.
5. Lethal means of bringing down Martian Manhunter are acceptable, but only as a last resort. Subduing him is far preferrable.
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NOTE: I am going to assume that most responses would include something about Batman exploiting the whole emotional flame vulnerability thing. While this can be a legitimate tactic, describe how it will be executed to best effect.
Something like, "Batman burns an orphanage in front of MM. End of story." doesn't cut it.