Was he the Witches Son? The title would have you believe it, the fact is that Elphaba didn't know for certain, and she certainly never treated Liir as her son, more of an inconvenience.
This book starts with the discovery of a young mans broken body found in the middle of no-where. He is taken to a mauntery, where the Maunts believe he will be dead before long - but old Mother Yackle thinks otherwise. So a young Maunt called Candle plays music to him and while she plays the past is revealed. The story of how Liir left Kiamo Ko with Dorothy and many years later ended up in the Mauntery.
The driving force behind the story is Liirs search for Nor - the only member of Fiyero's family that ever showed any kindness to him - the reasons behind that need are unclear - she could be his half sister afterall and maybe that's what he wants - family. Not knowing who his parents really are - treated more like a servant for most of his life. He's confused by things he feels because he doesn't have anyone to show him the way.
But life has other plans for Liir - unable to find Nor (even risking a trip to Southstairs prison in the Emerald City - with the help of Glinda and Shell) he enlists in the home guard - but finds himself used in a particularly ugly incident involving the burning down of a village. Here ends his military career and instead he tries to understand who he is and what he wants and he tries to do the right thing when he can - be it elminating a stable of Dragons or helping Princess Nastoya to end her pain.
But history has a way of repeating it's self and just like Elphie couldn't remember giving birth to a son, Liir possibly ends up fathering a child - one he doesn't remember making. The question of the parentage of both is answered in the final sentence of the book (although it could have been answered in the Mauntery - as Liir ends up in the same one where he was born).
Elphaba casts a long shadow on everything - her presence is palpable at times and Liir is left holding the baby.....