World Without End by Ken Follet 

The second book in the Pillars of the Earth that takes place four generations later and pits descendants of Tom Builder on two sides.  A group of children, Merthin, Caris, Gwenda and Ralph are exploring the forest, where they should not be, stumble upon a scene where two men-at-arms are attacking a knight. Ralph grabs a bow from his brother, Merthin, and sends an arrow into the eye of one of the men.  The knight dispatches the other but is wounded.  All but one of the children run away.  The knight gets the remaining child to help him dig a hole and bury a secret.

The knight becomes a monk, saving his life, but not his arm.   Merthin grows up to become a carpenter and a builder.  Ralph grows up a bully and a squire.  Ralph gets in trouble for raping a serf girl, is sentenced to death and runs from the court to become an outlaw.  When he is caught, the local Earl commutes his sentence in order fulfill the King's demand on men for his war on France.

Merthin is entrapped by the pregnant daughter of the man he is apprenticed to.  Because he refuses to marry the girl, he is fired, just two months short of becoming a journeyman.  But he is a better builder and eventually becomes richer than his former master.  He is also in love with Caris, but she won't marry him.

All this is against a backdrop of the plague and Caris, because she has a mole at her groin is accused of being a witch.  To save her self, she has to agree to become a nun - even though she does not really believe in God - mostly because she can see the corruption in the local priory.  Caris studies what happens when different methods are tried on the sick.  She does not agree with the centuries old methods of bleeding patients.  She wants to use masks and keep the sick away from the healthy to try to keep the plague from spreading.

Eventually, her methods are used, a more trustworthy man is made prior, Merthin succeeds in Florence and England with his dreams as a builder, replacing a crumbling tower on the cathedral with the tallest tower of the time, Caris is released from her vows and they marry and run a hospital.