Yes, this was a really geeky (maybe too geeky) old-school Who reference, not a season-arc villain. It's a new origin story for the Great Intelligence, who Patrick Troughton's Doctor fought twice in "The Abominable Snowmen" and "The Web of Fear", respectively set in the Himalayas in the 1920s and in the London Underground in the late 1960s. ("The Web of Fear" is also the first appearance of the then Colonel Lethbridge-Stewart and probably the event that caused UNIT to be created.) Unfortunately both of those stories are mostly destroyed, although two episodes of the first and one of the second survive and we have audio for all of them.