Someone is murdering all the demons in LA, even the harmless ones. While Angel and Wes investigate the killings, Gunn begins to suspect that his old vampire hunting friends are behind the attacks. He feels torn between his old gang and his job with Angel Inc. But when the gang attacks Caritas, everyone is in danger.
While investigating some mysterious deaths, Angel switches bodies with a old guy named Marcus. Marcus immediately takes over Angel's life, while Angel is stuck in a retirement home. When Marcus realizes that Angel's body gives him vampire powers, he decides that they only way to keep it is to get rid of Angel once and for all.
Fred's parents show up in LA and Team Angel is instantly suspicious of them. They seem a little too... Normal. Fred hiding from her family and has run off. In order to find her again, Team Angel and the Burkles will have to work together. They'll also have to battle some demons and pay a visit to Lorne. And Fred will have to decide where she really belongs now.
A guy named Billy is infecting men with primal misogynistic impulses. When he touches men, they attack any women that they come across. Lilah is beaten and several other women wind up dead. Cordy and Angel try to track Billy down. But, when Billy's blood infects Wes and Gunn, it might be too late for Fred. And when Billy touches Angel, Cordelia could be in trouble, too.
Darla comes back to LA, bringing Angel news of their baby. As Team Angel tries to find out how a vampire pregnancy is even possible, Angel must deal with his growing feelings for Cordy and his new fears about what sort of "child" Darla might be carrying. Meanwhile, one of Angel's old enemies arrives in LA looking for vengeance.
Team Angel continues to try and deal with Darla's pregnancy. When Wolfram and Hart finds out about the baby, the law firm decides to steal it for themselves. Meanwhile, Holtz is determined to kill Angel and arrives at the Hyperion looking for revenge.
As Darla goes into labor, Team Angel tries to help her deliver the baby. Unfortunately, there are some unforeseen problems. Angel is captured by Holtz, who learns that Angel now has a soul. In the end, it's up to Darla to bring Angel's son into the world, no matter what the cost.
With the birth of Angel's son, the gang returns to the Hyperion to regroup. There are countless demons, humans and lawyers after the baby now, and Angel is scared to let the kid out of his sight. Team Angel will have to help him keep Connor safe and defeat the baby's enemies. Meanwhile, Holtz finds an ally, a vengeful woman named Justine.
It's Cordy's birthday and a particularly intense vision knocks her out of her body. As Team Angel tries to help her, Cordy is stuck in an astral plane unable to communicate. When a guide shows up and offers Cordy a deal, she has to choose between getting everything she thought she wanted and her life with Angel.
With his new son to consider, Angel begins worrying about paying the bills. His pursuit of money worries Cordelia, who is concerned that Angel will forget his mission to help the helpless. As Team Angel is spread thin, covering as many paying cases as possible, several members are put in harms way.
When a famous dance troupe comes to LA, Angel is thrilled. He drags Gunn, Fred, Cordy and Wes along for a night of ballet. Unfortunately, supernatural forces are afoot at the theater. Meanwhile, Angel is scared to admit his real feelings for Cordy. Wes & Gunn both continue to fall for Fred and she finally kisses one of them.
Wesley is depressed as Fred and Gunn grow closer, and the Groosalugg's arrival irritates Angel. Angel is jealous when Cordelia and the Groosalugg search for a way to be together without endangering her visions. Meanwhile, Wesley focuses on translating a scroll about Connor and he's soon horrified by what it suggests.
After translating the prophecy, Wesley is terrified. It says, "The father will kill the son," meaning Angel will kill Connor. Meanwhile, Gunn and Fred investigate a vampire nest, while Holtz amps up his plans for vengeance. Wes tries to disprove the prophecy, but all signs seem to point to disaster.
As Wesley struggles to come to terms with the prophecy, Angel's behavior grows more and more erratic. The crew at Angel Inc. is concerned as Angel's moods swing from giddy to furious with no provocation. While Holtz, Lilah and Shajhan continue to plot vengeance against Angel, Wes takes drastic steps to keep Connor safe.
With Connor trapped in a hell dimension, Angel is willing to do anything to rescue him... Even make a deal with Wolfram and Hart. Meanwhile, Fred and Gunn search for Wes, who is gravely wounded. As Angel tries to save Connor, he learns some terrible new information about the prophecy.
As Angel grieves for Connor, Cordelia returns to LA and tries to comfort him. Meanwhile, Gunn is falling in love with Fred. But, he has to deal with a mistake that he made back when he was a vampire street fighter and it could ruin their happy future. Wes, abandoned by his friends and banned from the Hyperion, leaves the hospital by himself.
After performing dark magics back in "Forgiving," Angel knew there'd be a price and this is it. The Hyperion is being invaded by little slugs that dehydrate anyone they infect. As Team Angel tries to fight them off and save one of their own, they learn that something called the "Destroyer" is on its way.
Angel is stunned as Connor falls through the portal from the hell dimension. His son is now a teenager and, thanks to Holtz, he hates Angel. While Angel tries to get through to Connor, Lilah shows up at Wesley's apartment with an interesting proposition...
With Holtz back in LA, Angel Inc. is in for some problems. As Angel tries to bond with his son, Holtz reconnects with Justine. The two vampire hunters cook up a plan to turn Connor against Angel forever. Meanwhile, Wesley and Lilah spend more time together and Cordelia and the Groosalugg grow further apart.
In the season finale, Connor plots revenge against Angel. He blames Angel for Holtz's death and comes up with a plan to make his father pay. Meanwhile, Cordy realizes that she has feelings for Angel and Wes & Lilah make love for the first time.