This is a typical example of a Bacterial infection, normally followed by a parasite invasion during this time of the year, normally caused by bad water conditions. The Nitrites go up, the Koi's immune system goes down, the parasites go crazy and it is followed by a bacterial infection, causing Ulcers, sometimes referred to as "hole disease" like in your case, and you will probably see fin rot. It is caused by aerosomonas and pseudosomonas bacteria.
You should first look at the reason why you got a bacterial infection, and therefore, step 1 will be to check your Ammonia and Nitrite level. If not zero, do an immediate 35% water change and rectify the levels as soon as possible, as the fish will need perfect water conditions to heal.
Secondly, do scrapings for parasites and eradicate if present.
Thirdly, treat for the bacterial infection. Increase your salt level to 6 kg/1000 liter, do topical treatments of any wounds, and treat with Acraflavin, an anti bacterial medication and give antibacterial foods if available and if the fish are willing to eat.
Topical treatment can be done with Methialite, Mercurochrome, pure Malachite green or a Potassium paste directly on the wound. Cover it with Friar's balsem to waterproof the medicated wound.
If it is a large and expensive fish, consider an antibiotic injection(Baytril) which treatment has to be followed up. See the section under bacterial infection.
For more information, go to the bacterial infection section of this forum or view our website.
The photo of the scraping does not help at all. No parasites are present on the slide and a bacterial infection can not be viewed with a microscope. You will also not be able to see any parasites if the scraping was taken a while after the fish died. The slide looks scary, but it is purely water bubbles reflecting the light of the microscope.
The secret of bacterial infections are to treat as soon as possible, before it infects internally. If you see any red areas on the fish, consider it as a possible developing ulcer and treat immediately.
If one fish is affected, you can assume that the other fish are also infected. In your case, treat the whole pond.
If not successful, give me a call.