The Reference Desk/Cybermen merging universes

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In the Doctor Who/Star Trek: The Next Generation crossover comic Assimilation2, it is heavily inferred that the universes of the Doctor and Star Trek (and their whole histories, judging by the TOS crew's encounter with the Fourth Doctor and the Cybermen) have been merged together as part of the Cybermen's plot. But it's never explained exactly how this is accomplished. Does anyone have any theories? Also, at the end, the Doctor tells Captain Picard and co that with the Cybermen totally wiped out in the Trekverse, and with him and his companions about to depart, the two realities will separate and assume their correct forms, with the past changing so the Cyberman attack never occurs (though he adds that the Enterprise-D crew will remember it). Why does he say this?