The Enemy

The Enemy were the Time Lords' largely unseen opponents in the Second War in Heaven. Little was known about them. It could not even be said, for instance, whether the term described a species or merely a group of individuals.

Greyjan the Sane claimed that they were the cells of the first life to evolve in the universe, having been irradiated by temporal interference and then energised by a leaking bottle universe. The Eighth Doctor offered the more entertaining possibility that they were likely to be eventually revealed as "Yartek, leader of the alien Voord, carrying a big stick." (EDA: The Ancestor Cell)

They were known not to be either the Daleks nor the Krotons. (EDA: Alien Bodies)

The Enemy's agents were referred to as "reps", but there was no indication what, if any, significance the term had. (EDA: The Taking of Planet 5)

Behind the scenes

 * Despite reports to the contrary, the Enemy were never originally planned to be the Daleks. Other books in the EDA series make it clear that the Enemy cannot be the Daleks. The confusion arose in relation to a later BBC Books arc, culminating in Sometime Never..., which had been intended to feature the Daleks until legal issues prevented it.
 * The creator of the War arc, Lawrence Miles, was extremely dissatisfied with the culmination of his storyline in The Ancestor Cell, which was not written by him. He therefore created the Faction Paradox series which ignores The Ancestor Cell and is set in its own fictional universe.