Something is killing my fish!

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You did good. :) I;m hoping ofr a quick recovery from whatever it is that got your guys. It's horrible not knowing the why. But you're doing everything as best you can. It's a good sign that the fish is looking better.

Is there any chance the water in the main tank was contaminated by something? A cleaning agent or something in the air? exterminator, anything different go on around that tank lately?
 
Not that I can think of, My honest opinion is that this all started when i bought a raccoon butterfly. He was the first to go, i think whatever it was that fish had it and brought it into my system.

I always scoffed at the idea of quarantining fish for a while, if my LFS does it before they sell me the fish why would I need to. Well needless to say i learned that lesson!

Am i going to have to do anything to my main tank? im going to give it a good cleaning since i have to re scape the whole thing. Just leaving it with no fish really will make whatever is in there die? Should i turn the system off for a while?
 
I would do a large water change and keep it running. You might also wanna vacuum up the sand a bit, nothing crazy but just get the top layer and skim off that.

You may have to keep the fish in qt for over a month to guarantee that whatever was in there dies. I didn't add any more fish to my tank for 2 months after my mystery outbreak but I did leave the survivors in adn they never got any symptoms or anything. I think I got lucky it didint wipe out everything.
 
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