I take it that you are referring to the cracks?
Russell T. Davies' series had these central running themes too; the recurring 'Bad Wolf' words that Rose Tyler kept finding in the first series (it even appeared in Torchwood!) which culminated in The Parting of the Ways episode and the Doctor's regeneration from Eccleston to Tennant. There was also the 'Vote Saxon' paraphernalia that both the Doctor and Martha generally overlooked in the third series, which culminated in Last of the Time Lords and the Doctor-Master conflict.
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