Season 2
Season two started in September 2007. On the first day of school there is a race-riot which starts at Cassie's high school and separates her from Charles. The riot spills onto the streets of Lincoln Heights; from Jenn's nurse clinic, to Eddie's police job, to Lizzie & Tay's middle school. Lizzie, Tay and Tay's best friend, Johnny, lock themselves in the computer lab and later find they can't get out. Eddie and a young kid point their weapons at each other and the kid shoots Eddie in the leg. Lund fires a shot at the kid and hits him in the shoulder. Jenn manages to patch up all the patients, including her husband. Charles reunites with Cassie and Lizzie, Tay and Johnny get freed. Lizzie and Johnny start a relationship. Lizzie visits Boa, her ex-kidnapper and baby-sits his niece who ends up going to Child Services. Lund's new teenage daughter, Sage, starts at Cassie's high school and the two strike up a friendship. Unfortunately, their friendship crumbles when they get pulled over while driving Sage's mother's car.
The police find drugs in the car and Eddie and Lund interrogate their daughters. Sage claims the drugs belong to Cassie, but Cassie refuses to take the fall for it. Tay starts his music career, but he gets into trouble with his parents about it. Cassie & Charles' relationship intensifies, but Cassie wants to know more about Charles' stepfather, who finished his prison sentence and is now back in his mother's life. Eddie notices the tension and tries to help. Jenn quits her job at the hospital and starts working at a local clinic.
Cassie finds a job at the coffee shop and becomes attracted to Luc, the boss of the place and a producer for local R&B artists. Charles becomes jealous and breaks up with her, thinking he is holding her back. Cassie starts a relationship with Luc and Sage starts a relationship with Charles. Tay is introduced to a girl he likes and is also introduced to the world of alcohol and rehab. Eddie's father comes home and starts a relationship with the late Reverend's wife. Eddie's father, Spencer, finds the man who gunned down his wife and Eddie's mother when Eddie was thirteen years old. The murderer was a man who worked with Jenn and was friends with Tay. Spencer seeks revenge. Charles and Sage get into a serious car accident in the end of the season.
Season 3
The third season of Lincoln Heights premiered on Tuesday, September 16, 2008. Eddie and Jenn's relationship becomes stronger as living in the Heights gets harder. Lizzie gets accepted to a new school under a scholarship. Dana tells Eddie that she has a son named Nate. Tay's career of being a singer is working out great, but he ends up getting into trouble because of it. Charles proposes to Cassie, who originally says yes, but then starts to question herself. They both eventually decide to pledge eternal friendship to one another. Sage recovers from her coma and later runs for prom queen which she wins. Charles is voted Prom King. Mac, Charles' stepfather, attempts to kidnap Cassie outside of the prom, but fails when Tay stops him. Lizzie's best friend, Johnny Nightingale is killed by a hit and run driver. His loss causes Lizzie to fall into a depression. Feeling guilty over Johnny's death, she pulls away from Devin Kingston, whose father is the new reverend at the church. Cassie and Charles have sex on the school's stage which is set up for a Romeo and Juliet play. They end up being filmed by someone who was watching. Cassie later worries that she is pregnant, but later finds out it was a false alarm. Lincoln Heights is suddenly hit by a massive earthquake. Nate is trapped under a large beam in the Sutton home. Eddie tries to help him out and questions Nate about the father he never knew in order to distract him from the pain.
Charles' stepfather, Mac is killed during the earthquake when a massive refrigerator falls on him. He is conscious, barely, but Charles refuses to help him. Cassie is scared and uncertain, but Mac dies before they decide to help him. Eddie and Jenn later find out that Nate is Eddie's son. Jenn is devastated by this news and struggles to cope in this difficult situation. Many homes are damaged by the earthquake and fires have broken out all over Lincoln Heights, including the Sutton home. They gather what they can and leave as quickly as possible. Cassie asks Charles to get her sketch book out of the attic where he discovers a hole in the wall with $100,000. So he puts it in his bag and grabs the sketch book running out of the house. In the end of the season, it shows the family and Charles looking at the house, not saying a word about the money.
Season 4
The fourth and final season of Lincoln Heights premiered on Monday September 14, 2009 with 10 new episodes. The season starts with Charles and Cassie being charged for the murder of Charles' stepfather. There was not enough evidence, so the case was closed. But immediately afterward, the police check both Charles' and Cassie's homes for the stolen money that Charles has, but the money is safely stashed. Lizzie finds trouble when she is encouraged to join a community club. She starts rumors about a schoolmate and then apologizes and quits the club. Meanwhile, Charles discovers he received a letter from his father fifteen years ago, which his mother kept from him.
After obtaining his father's phone number, the two talk and decide to meet. Charles asks Cassie to go with him, but her parents forbid her. She ignores them and instead sneaks out to join Charles and the spend the night with him. Cassie leaves the following morning to face her angry parents, but Charles decides to stay in order to get to know his family. Lizzie makes friends with a Mexican boy while at a community recreation center. He gets very attached to Lizzie and agrees to let Lizzie take his special bear home to fix after another boy, who picks on him, tears it. While walking home alone, Lizzie gets attacked by a man who is after the teddy bear because of the drugs concealed in it.
Cassie finds out that Charles has kept yet another secret from her, which causes him to lose Cassie's trust. To cope with the pain, she decides to go to a popular club with Sage, Sage's boyfriend and Serge, who likes Cassie. While at the club, Cassie goes to the bathroom only to find Serge waiting for her. He tries to touch her, but she kicks him in the crotch. Meanwhile, Lizzie leaves the Outreach dance early after Andrew tries to kiss her during a song which brings back memories of Johnny. The next day, she seeks Andrew out to apologize for leaving early and to explain why. They end up sharing a kiss. The next episode starts out with a surprise visit from Grandpa, who develops a serious crush on the female pastor. He is devastated when he finds out she is engaged to former pastor, Deacon Jones.
Lizzie invites Andrew to meet her family, including her grandfather, who does not appear to be pleased with her new boyfriend. Later on, Cassie and Charles's relationship could be getting weaker. Charles's brother, Travis, visits where they get into serious trouble. Lizzie furthers her deep relationship with Andrew by including him in family activities. During a game called "Name That Bible Verse", things start to get a little out of hand. Deacon Jones accuses Lizzie of cheating and Grandpa embarrasses Lizzie by reacting aggressively. However, Eddie manages to calm things down before they get violent.
The next day, Lizzie and Andrew are having a private moment on the staircase when Grandpa's crush appears at the door. He apologizes for "flying off the handle" the previous night. She explains that she and Deacon Jones broke up because she feels like she was with the wrong man. Grandpa and the pastor share a passionate kiss, watched by Andrew and Lizzie. Tay meets his idol, Trey Songz, and gets to sing along on stage with him. At the very end of the episode, Jen is rushed to the hospital at the cause of a sudden illness. While Jen is in the hospital trying to recover, Cassie tries to decide where the future will lead her and Charles. It is revealed later, as Jen is making a full recovery, that the virus came from the site of the torn down crack house, and not from the clinic as was feared, so the clinic stays open.
Towards the end of the season, Charles decides to join the Army and Cassie considers attending Pratt, a prestigious fine arts/design school in New York City. However, before making their decisions, Cassie and Charles decide to get married and the Sutton and Antoni families race to the ceremony. Just before the ceremony at the courthouse, the mystery of the $100,000 gets solved. It turns out the money was a payoff of an old murder due to a racist prank committed by Eddie's chief when he was a child. A former inmate on parole, Sid Glass, claims the money and gives half to the Sutton family because of their generous help and effort to support her.
Tay writes a hit song dedicated to Nate Ray called "Fight for You." Nate Ray later sees Tay performing his song on a television news story and tells Jen that he sent the song to his army buddies and it went viral. In the end, Cassie and Charles don't end up getting married, but have an engagement party where their loved ones offer them blessings for a potential wedding in the future. Cassie's father attends with Charles' parents. Charles decides against going into the army and instead accepts his father's offer to pay for him to attend a good college.
