Funny how today so many bioweapons place a strategic emphasis on E. Coli for the delivery.
So if I just conjecture wildly (really wildly) ...
1. Neanderthals kill the local magistrate "Humbaba" for the Melonheads in 110,000 B.C. after he encroaches on Amud forestry lands (cedar groves). This triggers off many local skirmishes including the killing of a ritual bull by Neanderthals who have broken their ancient habits of keeping to themselves. The Melonheads take their first ever planet wide referendum and the decision is made to finally end the longstanding truce with the wildly independent Neanderthals. They respond with aerial spraying of the Caucasus and surrounding regions with a deadly pathogen.
2. Much later, after surviving Neanderthals begin to bounce back, a powerful nuke is used to detonate the Toba supervolcano at 80,000 B.C. and trigger it's eruption. Melonheads retreat into their underground megalithic structures and dolmens while the world experiences a winter that lasts upwards of twenty years. They think this should finish off the drastically reduced rodeo clown population.
3. Realizing that both of these extreme measures have failed to get the job done, the Melonheads around 60,000 B.C. deploy their most dangerous genetically engineered organism at the southern tip of Europe - Homo Sapiens. Where germs and bombs failed, Sapiens gets the job done. Melonhead genius prides on itself on always winning, no matter what circumstances. It's not just that their final solution has finally worked but Sapiens himself is deliberately designed so that he will never present a threat similar to the Neanderthals - he has had his soul, volition, sentience completely snipped out of his genetic code.
4. The only catch is that as Sapiens conducts his campaign north he takes female war captives from the Neanderthals. His inadvertent interbreeding program has the effect of introducing Neanderthal genes into his own population permanently as a subspecies. Some humans retain some limited capacity for independent thought and self-awareness as a result.
5. The great irony is that over the ensuing 40,000 years, the Melonheads wane in a process of attrition to diseases from inbreeding and lose substantial social power in the aftermath to the new Sapiens-Neanderthal hybrids, an aggressive species which is never as easy to manage as their slave classes in former days. Where the Neanderthals failed, natural forces conspire to reduce the "pure" Melonhead stock to a few lonely pharoahs in the last days of Egypt, tragically trying to restore the old caste system of their death cults and monolithic building societies. It turns out, the bell tolls for thee, oh egg-domey one.
... now you have to admit, deranged and as far-out as this explanation sounds, it would answer so many questions if it were true. It is not that I believe it exactly, it is that I permit myself the luxury of speculating on this subject. The orthodoxy has shown itself to be incapable of offering any coherency to it's narratives so I have tried to fill in the vaccuum, that's all. The real "truth," of course, is probably something we can never know. We can only guess at these things at best. The only thing we can say with genuine certainty is that the story they teach us in school is absolute hogwash.