Lily Rivera was the estranged daughter of the Puerto Rican crime boss. She got pregnant by Miguel Morez when she was sixteen. Her father put a hit on Miguel and his family smuggled him out of Puerto Rico. Lily was sent to a convent and as soon as the baby was born her father forced her to give it up for adoption. Thinking that Miguel was dead and his son lost to her, she wouldn't have anything to do with her father.

When L&B Records launched Miguel's singing career with a concert in Puerto Rico, Sonny Corinthos, a partner in L&B Records, decided to search for Lily, Miguel's lost love. Sonny found Lily and convinced her to come to Port Charles and resolve her feelings for Miguel.

Lily got a teaching job and moved into a room over Kelly's. Lily and Miguel tried to recapture what they had as teenagers and got engaged. Lily and Sonny became close friends, which made Brenda and Miguel jealous. Lily and Sonny were also jealous of Brenda and Miguel who were making a steamy video for Miguel's hit song. Sonny then found Lily's six-year-old son by Miguel and Sonny and Lily flew to Puerto Rico to meet her son Juan. After meeting the Santiago's, and seeing how happy he was, Lily decided to leave her son with his adopted family.

Sonny asked Lily to take contracts for L&B over to the gatehouse for him, as she approached the window she overheard a conversation between Lois and Ned Ashton and Mac Scorpio. They had convinced Brenda to wear a wire to get information on Sonny's mob dealings. Lily warned Sonny, he frisked Brenda, found the wire and broke up with her. Miguel was disgusted with Lily and they fought over her friendship and loyalty to Sonny, which put a strain on their relationship and ended their engagement.

Sonny and Lily continued to hang out together; he went apartment shopping and took her along. When he found the Penthouse Apartment she agreed to decorate the apartment for him, they made love for the first time in the penthouse. Lily realized Sonny still loved Brenda and convinced him to go talk to her and try again. They went to Kelly's and went upstairs, Lily going to her room and Sonny to talk to Brenda. When Lily and Sonny got in front of her door, Miguel and Brenda, who both lived above Kelly's, was coming out of the shower together after having made love. That was the end of Brenda and Sonny and the beginning of Sonny and Lily.

Sonny got arrested and ended up in jail facing prison time. Lily went to her father and begged him to get Sonny out. Her father realizing that she loved Sonny and believing he would be a good son-in-law offered him a deal. He would make all of the evidence and witnesses against Sonny disappear and he would marry Lily and take care of her. Lily truly loved Sonny and hoped he would come to love her in time. Sonny really cared for Lily and trusted her completely so he thought he could be a good husband and they could make the marriage work.

After they got married Lily insisted on keeping her job as a teacher and she would not let Sonny's bodyguards shadow her. A couple of incidents happened because of this, which landed Lily in the police station where she became friendly with Mac Scorpio, Taggert and Detective Garcia. She and Sonny had a lot in common and when they fought, they fought in Spanish. She had a profound effect on the men in Port Charles. Through her efforts Sonny and Mike mended fences; she sat with Stone who was dying of AIDS when Sonny and Robin rested; explained things to Jason and formed friendships with Luke Spencer and Justus Ward. She tried to build a bridge between Taggert and Sonny and became too friendly with Detective Garcia causing Sonny's jealousy to surface. None of the men in PC thought Sonny deserved Lily.

Brenda was devastated when Sonny married Lily; she was determined to get him back so she convinced Jasper Jacks to help her make Sonny jealous. They kept showing up every where Sonny and Lily went. One weekend they followed Lily and Sonny to the mountains and Brenda and Sonny got caught in an avalanche while skiing and had to seek shelter in an abandoned cabin. Lily went to Jax for help in finding Brenda and Sonny, after that Brenda and Sonny declared their love for each other and could no longer stay away from each other. This did not please Lily's father who was having Sonny watched by his accountant Harry Silver who had become Lily's surrogate father. Lily's father threatened Brenda then tried to kill her.

Unable to get Brenda out of his heart, Sonny decided to leave Lily to be with Brenda and go into hiding but before he could tell her his decision, she told him she was pregnant. Sonny went to Brenda and told her he was staying with Lily and there was no future for them. Because Sonny didn't react the way she hoped over her pregnancy Lily left him to go back to Puerto Rico. Sonny followed Lily to the airport and begged her to come back to him and give him another chance to be the kind of husband she deserved.

Lily's father thought Sonny was not living up to his promise of being a good husband and unaware of Sonny's newfound devotion to Lily or her pregnancy he decided to get rid of Sonny by placing a bomb in Sonny's car. After a celebration party at Luke's Club where they announced the pregnancy to everyone, Lily went to get the car, which blew up when she started it leaving Sonny devastated. It was during Sonny's period of grief that he realized how much he loved Lily.

Sonny went to Puerto Rico to see Lily's father, who had a heart attack when he found out he had killed his pregnant daughter. Sonny gave him a gun to kill himself and his territory became Sonny's. Not being able to touch her money, Sonny donated Lily's entire estate of 30 million dollars to GH to build the Stone Cates Memorial Aids Wing.