Lee and Donna lost each other while being rescued from the computer, Donna's last words to him being a promise that she would one day find him. Donna was led to believe that Lee wasn't a real human. It turned out that he was a human after all, but since he had a stuttering problem, he couldn't call out to her when she left with the Tenth Doctor.
Behind the scenes
In the DVD writer commentary on Forest of the Dead, Russell T Davies and Steven Moffat revealed that the original draft of the script would have revealed in his final scene that Lee was assigned female at birth in the real world. However, it was cut because they didn’t feel that it had been made clear enough that individuals were able to choose their appearance inside of the virtual reality of the Library, and that it would therefore be too confusing in the split-second framing of the reveal that the episode's structure necessitated. This would have made Lee one of the few portrayals of an explicitly transgender character on the show.
Unrelatedly, on the commentary of The End of Time, Russell T Davies noted that the writers toyed with the idea of bringing Lee back as Donna's fiancé, but gave up because it "wouldn't really have made sense" in terms of the timeline.