Bigred:
After you follow REC's advice and have the fish in a hospital tank, I think you have some water issues to address. It should not be tea-colored. I suspect that your waterlillies and other plants are potted in a medium which is leaching into the water. It is entirely possible to keep smaller sized koi with plants, but there is balancing to be done. One of the things you have to do is let the newly submerged soils "age". For a period of a few months, all sorts of substances are released into the water. (These might have hurt the immune response of your koi, contributing to your current situation, or may have a more direct involvement, or may be irrelevant to your problem ... don't know.) You will need to perform more frequent and larger water changes to keep the water uncontaminated. Eventually, the soil becomes a submerged soil and the contaminants released are not so severe. (But do not follow the typical watergardening advice of adding fertilizer to the lillies monthly ... fine for the lillies, but not for the health of the pond with fish.)
If all the fish are placed in a hospital tank, I'd suggest you perform as close to a 100% water change as you can and keep on top of the water quality parameters so your koi have good quality water to return to.
[I do not believe keeping larger koi with plants is workable without too many compromises. So, the purists ready to jump on me for suggesting they can be successfully kept together, please note that I said "smaller sized koi".
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