It would be tricky. I am going to assume that the actions were taken before the war. Depending upon who Krell is he could have done this as his last act out the door. Perhaps he didn't even do this to kill Prime base but to kill the whole project. Perhaps he assumed that ALL Project members, field teams abd base personnel would get this vaccine or drug cocktail before they were frozen so they would basically wake up just in time to die. This would be a very Krell thing to do. He was proabably pissed to no end that the teams he captured were not infected with the trajan horse. At that point he may have guessed that if the tricked out vaccine had not been destroyed it was at the Bases. He would give his guys doses of the real vaccine and then infect every captured Morrow Project Member with it and see what happened. They probably put some sort of tracking device on the infected people to see where they went. This would be quickly spotted and removed by standard protocals before the victims go anywhere near any base entrance, but would add to the concern in Prime. It would now be obvious that they were facing a prepared tech savvy enemy with some serious resources.
I think the refugee camp idea works fairly well. I would put it down on the valley floor though and the base is accessed through the long tunnel from the fake town ot paper recycling facility or whatever.
The colony is placed fairly close to the entrance, maybe a few hundred yards. The hostage/vector plan goes as in the book. The Krell do have a bomb. It was a variable yield weapon. The trapped Prime Base member, knowing the base could take the results (since it is ten plus miles away and under a lot of rock and such) dials up the bomb to maximum yield and detonates it.
This leads to a large crater which should be right over where Prime Base was thought to be. The follow on Krell teams find this much larger crater (filled with water) and absolutely no other evidence that Prime Base exists.
Krell's force keep a watchful eye out for any Morrow Team activations. For fifty years they keep a strict lookout for Morrow radio Traffic, for multiple team activations or for anything else that would indicate the Prime Base had survived and was functioning on sone level. During this period Krell teams cross and recross the area in which they believed the base was located. Heck to be certain they may pop a couple of other nukes or whatever.
In any case the Krell organization is absolutely certain that Prime Base was destroyed. After 150 years without the MP waking up except by internal means (see my post on that) they have no reason to suspect Prime wasn't effectively destroyed 3 years after the big OOPS.
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