The Enemy

The Enemy were so called because 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 they possessed an opposing Web of Time contrary to the Web of Time which the Time Lords had constructed and imposed on the universe.

They did have a specific name and a specific leader, but the Time Lords were loath 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). 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 Taking of Planet 5) They are more accurately described as a living series of events in constant temporal flux. (FP: The Book of the War)

They are known to not be the Osirians (MB: Coming to Dust), the Daleks nor the Krotons. (EDA: Alien Bodies) The Doctor's TARDIS claimed that the Doctor once found out who the Enemy were, but erased his memory so that he didn't change his people's future. The Enemy's agents were 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 occurred 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." and is represented by a total absence of anything on the recovered film. Not blackness, just emptiness and the background filmstock. (FP: The Book of the War)

Another encounter occurred when Marcus Americanus Scriptor encountered something while hunting a renegade Time Lord who had escaped the War by jumping into a parallel universe. The creature was intelligent, bragging that nothing any human could conceive could harm him, especially time-based and ritualistic weaponry. However, its masters/creators/fellows never considered that it might be attacked with something so utterly primitive as a simple sword, which led to its death when it was attacked with one. It was described as being constantly in flux, and was implied to be, at the very least, a very powerful enemy agent, if not an enemy itself. (FP: Warlords of Utopia)

Compassion stated that the Enemy was merely a distraction and that the true threat to the Time Lords would come from within. She later hinted the emergence of House Lucia was the true threat to Gallifrey. House Lucia's connection to the Enemy was only hinted at by Compassion and her companion Carmen Yeh and was not elaborated upon. (FP: The Book of the War)

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. Miles was so dissatisfied with this storyline that he created the Faction Paradox (series) which ignore The Ancestor Cell and are set in an alternate timeline to the mainstream Doctor Who universe.