Harmony is having trouble adjusting to working for Angel. The other employees of Wolfram & Hart ignore her and she's feeling depressed about her life. After a night out with Fred, though, Harm's troubles are about to get a lot more serious.
Lindsey and Eve continue to plot against Team Angel. Lindsey approaches Spike, telling him that the Powers That Be have selected Spike to be the new Champion now that Angel is working for Wolfram & Hart. Meanwhile, Angel is caught in a series of hallucinations and can't wake up.
A psychotic vampire slayer has escaped from her asylum, and is now on the loose in Los Angeles. Angel and Spike are on the hunt for her, before she does more damage. Once she is found, looking for pieces of her past, she believes that Spike was the man who drove her towards insanity, and wants to seek revenge.
Angel's past comes to haunt him. An ally from World War II takes Fred, Gunn, and Wes hostage while seeking Angel. This is the only vampire Angel sired after he got his soul back. Angel relives the past and must determine his future.
Angel and the gang set out to foil an evil puppet show that is sucking the brain power of all the children who watch. During their fight, Angel is turned into a puppet himself and must rely upon his friends in order to reverse the spell which holds him at one foot tall.
When an ancient sarcophagus arrives in the laboratory at Wolfram & Hart, Fred opens a small compartment and is infected by an ancient disease that slowly begins to kill her. As Angel and Spike travel across the world in order to help her, Wesley slowly begins to realize that there may be no stopping this disease.
As Angel and the gang try desperately to bring Fred back, Wesley begins to understand that the ancient demon Illyria, now fused with Fred's body, is here to stay. Exhausting all options for saving Fred, the gang switches gears to stop Illyria and her plan for global domination.
Angel, Spike and Gunn travel to a surprisingly unusual hell dimension to free Lindsey and find out what he knows of the Senior Partners' ultimate plans. With Illyria's army defunct and her plans averted, the gang accepts her as a dubious ally. Wesley, volunteering to be her guide and mentor, falls slowly into depression and self-destruction. Meanwhile, the Senior Partners send a new, unstoppable force, a new liaison and businessman, named Marcus Hamilton, to find Eve, and Gunn makes an important decision in an attempt to protect his friends... and save his soul.
Parents bring their son to Wolfram and Hart to try to make sense of their son's superhuman abilities. Team Angel wants their assistance, but Angel refuses, because it's his son Connor. A demon is after Connor, but without his memories of his old life, he doesn't have much of a chance against the demon. True memories are revealed for Connor and a member of Team Angel
Illyria begins acting more strangely than usual. After she rescues Gunn from the suburban hell dimension, she begins displaying more power. After a hint from Hamilton, Wesley discovers that Fred's body is insufficient to contain Illyria's power, and she is about to explode. Meanwhile, Angel discovers that she is unintentionally leapfrogging through time, and uses it as possibly the only way to stop her. Also, Gunn begins to have suspicions about Angel being corrupted when he allows a demonic brethren to accept a pregnant young woman's baby as an upcoming sacrificial ...
Angel and Spike's mission to help resurrect a demon gang leader in Italy is made more complicated when they learn that their former love, Buffy, might be in danger. Meanwhile, when the Burkles make a surprise visit to Wolfram & Hart, Illyria solves the problem by showing Wesley a frightening talent- a talent that challenges his own moral standing.
The Team have reason to believe that Angel has been utterly corrupted with power when they find evidence that he has joined the Circle of the Black Thorn, the most evil of secret societies. Wesley, Gunn, Spike, and even Illyria discover some surprises when they urge Angel to side with the forces of Good again.
In the series finale, Angel reveals that his questionable moral behavior has been part of a bigger plan: to destroy The Circle of the Black Thorn and show the Senior Partners that the power of good can still make a difference. Wesley struggles with helping Illyria adapt to the world, scolding her for her attempts to take on Fred's form. As Gunn continues his quest of self-discovery, Lorne becomes more aware of the lack of happiness in the world. Harmony attempts to seduce Marcus Hamilton for information, Lindsey makes an important decision regarding his alliance, and ...