He is not even named or mentioned in the first two novels, yet he is the ultimate main antagonist and Bigger Bad of the entire trilogy as a whole because of how he commands the Magisterium, and thus the whole Church, (including the General Oblation Board) and he subtly and invisibly orchestrated the events of the first two novels - he tried to have Lord Asriel assassinated, which led to the events of the first book, and he set the Magisterium agents to hunt down Will's father, thus orchestrating the events of the second book. He is the secret main antagonist in the trilogy.
In the Trilogy
He wants to abolish Free Will and is very determined to hunt down and kill Lyra, the protagonist, as she is Eve reincarnated and as being Eve, the first woman, Lyra will fall to what Hugh calls the "Original Sin". So he sends out a man named Father Gomez to assassinate Lyra with a shotgun to the head.
Later, Hugh travels to Geneva to see the nuclear testing of an interdimensional bomb whose explosion will resonate through every universe and destroy Lyra. Hugh is killed in an invasion on the base before this can happen, but although the bomb does detonate, it doesn't kill Lyra because her mother, Marisa Coulter, took a small lock of her hair which was going to be a vital part of the bomb.
As Lyra opens a gate from the Underworld into the Multiverse, it is presumed Hugh's ghost went through the opening and became one with everything.
Personality and Appearance
Hugh McPhail was an uptight and very business-like man, paying no heed to anything which he deemed frivolous, and completely eschewing any form of lightness or laughter in his life, befitting a very militaristic regimen in which he drank only water and ate only bread or fruit, "he would have been fat had it not been for the strict diet he imposed on his body" and his daemon is a lizard, meaning that he himself is very sneaky, cunning, indescribable, and malicious. He values literally nothing except his ultimate goal of abolishing Free Will. Marisa Coulter aims to seduce him but she finds out the hard way he is immune to such temptation.
Hugh McPhail was a force to be reckoned with, and yet he was somehow fair. He included in his ranks all types of generations, old and young, black and white, male and female, yet this may have simply been to appear good to the wider world as a whole, with Asriel dead he may have abolished his court altogether and moved in with the Authority. He is the one who started the General Oblation Board, of whom Marisa Coulter was the director, as he wanted to kill off Free Will and Original Sin in every child in his world.