On Wednesday, a team of marine biologists removed about 20 pounds of fishing nets and ropes from the whale's tail. She then appeared to head out to sea, presumably to resume its migration north to Alaska, but returned to the harbor on Thursday morning.
Marine biologists believe she was sick when she first entered the bay and was looking for a place to die.
Lily, estimated to be about 4 to 5 years old, was emaciated, indicating she hadn't been feeding. She also showed signs of inactivity.
Rick Baker from the Ocean Institute in Dana Point said active gray whales break off lice and barnacles when they feed at the bottom and come up to breach.
"But Lily had so much lice and so much growth on her. I don't think she was very active for a long, long time before she came to Dana Point. She was already suffering from something," he said.
Barker said Lily had a curve in her spine, possibly from an injury or a genetic defect.
As more experts got a closer look at the whale, they also got a better idea of what may have caused her death.
"We had a real hard time seeing how much rope was left on her so it was really important for us to get up there with our first chance to really see that," said whale expert Barry Curtis. "I could see the injury on her tail; her tail was broken so regardless of how much rope you got off, the ropes through the last three or four weeks had probably sawn through her control mechanisms so her tail was pretty much disabled."
So many people were saddened by Lily's death; they had hoped the whale would regain strength and head up the coast.
A necropsy will not be performed to determine the exact cause of death.