I love mind-bending arcs! The mind bendier the better. Scary, warped, funny, that's what I like.
Right, then, I am
going to recommend you the Faction Paradox/War arc. This was a foregone conclusion, because I love it beyond measure, but we shall pretend otherwise.
See, before the Daleks wiped out the Time Lords, there was a completely different Time War. And it was great.
Humanoid TARDISes! Time travelling voodoo cults! Conceptual entities that
oh bugger am I in one of those forum things again? sod that for a game of soldiers, I'm off interpose themselves within your local culture! The Celestial Intervention Agency gone completely batshit! An unknown Enemy against which the Time Lords are fighting in the future! The Doctor's own timeline at risk! Entire human cultures turned into weapons! Searing condemnations of the Doctor's failure to overthrow evil regimes here on present day Earth!
OK, the last one of those is possibly less exciting to most people than the rest, but I like it.
Start with Alien Bodies (no prior knowledge needed beyond the fact that the Doctor's companion at this point is called Sam -- imagine a generic young blonde girl companion a la Rose without any Billie to flesh it out and very uneven writing), if you can get hold of it, then you want Unnatural History, Interference (a two book epic crossing over with the Three era), and The Taking of Planet Five. The last two books to wrap it up are The Shadows of Avalon and The Ancestor Cell, but both of these represent something of a decline.