The Enemy

The Enemy are so called in that they were the Time Lords' opponents in the Second War in Heaven.

They were neither one specific species nor one specific political viewpoint. They were rather a process in themselves, and a version of history contrary to that which the Time Lords' Web of Time had imposed on the universe.

They did have a specific name and a specific leader, but the Time Lords were loathe to refer to either. Not because they feared speaking the names, but because conceptualising them in those terms would be to misunderstand them as something concrete, rather than as a series of events. (FP: The Book of the War)

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 (EDA:The Ancestor Cell), while the 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 Taking of Planet 5)

They are known to be neither the Osirians (MB: Coming to Dust), the Daleks or the Krotons (EDA: Alien Bodies). The Enemy's agents have been referred to as 'Reps', but there is no indication of what exactly that term might be abbreviating. (EDA: The Taking of Planet 5)

A rare instance of direct contact with the Enemy occured to Chris Cwej during his intervention in the filming of Mujin: The Ghost Kingdom. The cryptic exchanges that passed between them ended with the words, "The Scourge. Harvey. Hermes. The coolest character is the one whose face you never get to see." (FP: The Book of the War) and is represented by a total absence of anything on the recovered film. Not blackness, just emptiness and the background filmstock.

Another encounter occurs in Warlords of Utopia when Marcus Americanus Scriptor encounters something while hunting a renegade Time Lord/Member of the Great Houses who had escaped the War by jumping into a parallel universe. The creature was intelligent bragging that nothing any human could conceive of could harm him. Except a length of cold steel because it's so primitive that the creature nor it's masters/creators/fellows never considered that it might be attacked in such a manner (which is a recurring theme in the novel). It's described as being constantly in flux, and implied to at the very least be a very powerful enemy agent, if not an enemy itself.

Behind the scenes
Despite reports to the contrary, the Enemy were never originally planned to be the Daleks. Other books in the 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.