That was a disappointing ending. I guess the series was indirectly cancelled by being forced to wrap the series up even if it meant to create lose ends. I have to admit that I was surprised when the kids were stucked in the future. It probably means that the world was ending because of some ridiculous world disease, some kind of virus that kills off all current species and mankind and the whole island was built on the hypothesis that the kids will restart civilization by arriving on the island in the next 100 years. In order to improve the odds for a safe landing, they built the island on a huge scale and repopulated the island with extinct species which proved to be immune against the raging virus.
This explains why everybody died and why they had the green blob in the base in the first place, as this was a test subject to find a cure against the disease. But some psycho decided to release the virus on the island as well, killing off all personal. So when the kids appear together with the air plane, all of mankind are already dead thus giving the whole series title its actual meaning: Cage of Eden - The garden where everything begins, once again.