After giving birth to Jasmine Cordy fell into a deep coma and she was in hospital for most of Seaon 5, the group trying to get Cordy to wake up. Until when the Powers That Be gave Cordy a chance to come back and steer Angel in the right direction in "Your Welcome"
She's in a coma in Wolfram & Hart's medical facilities for the first half of S5, after giving birth to Jasmine. In the episode You're Welcome, she dies. However, the audience doesn't know this at first. She appears returning to the rest, reminding them of their purpose and encouraging them to fight Wolfram & Hart again. Just before she leaves, she and Angel kiss. Then once she's gone, Angel receives a phone call saying that Cordy had died that morning, and he realises that the Powers That Be had allowed her one last visit to put them back on the right track. Later, it's also revealed that she passed on the visions, for one use, to Angel when they kissed.