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Id have to say the Marrine getting harvested theory is more plausible than the finding other Plodex eggs theory. Didnt the Master imply that Marrina and her "mate" were the only two of their kind left alive on Earth? And that he looked around enough to be sure?
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It was implied that Marrina and her mate where the only surviving eggs. We know Gladys smallwood triggered Marrina to hatch so I wonder what triggered her Mate. (From the looks of him, probably seaweed or some other aquatic fauna).
It was also just written that 98% of the eggs where destroyed. I can't rmember the exact figure the Master qouted when he told Marrina of her heritage, but I'm sure it was more than a hundred million, so that would suggest that anything upward of two million may have survived. It is quite plausable that the Master was not aware of these few extra eggs, because they hadn't become active when he searched.