Conor is first seen in 1997 when his aunt Pauline Fowler tracks him and his mother Maggie Flaherty down in Ireland after she discovers Maggie is the sister she had never known about. Conor also has a daughter, Mary Flaherty, from his first marriage but he doesn't get on with her.
When Mary decides she wants to move to Walford with Pauline, Conor also follows her. In Walford he works as a mechanic for Phil Mitchell and as a loan shark 'heavy' for Annie Palmer. He tries to compete for Annie's affections along with Phil, but Annie isn't interested.
He then falls for Ruth Fowler, the wife of Pauline's son, Mark Fowler, after her marriage to Mark has fallen apart. Eventually Conor has a secret affair with Ruth, but after they have unprotected sex, he becomes fearful that Ruth will become pregnant and insists that she takes the morning-after pill. Ruth protests and eventually lies that she has taken it. The affair ends, but she does indeed become pregnant. When she discovers this in January 1999, she decides to keep the child. When Conor's daughter Mary accidentally reveals this to Mark, he is furious and hurt and goes after Conor, beating him up and informing him of the pregnancy. Conor offers to resume their relationship and bring up the child with Ruth. They decide to move to Scotland for a new life, so they leave Walford in February 1999 with Mary