Sometime during the years that USS Voyager was lost, she became involved with Starfleet Intelligence, becoming a covert agent. She used her career in music as a cover where she could get close to certain people. When Kim returned in late 2377, they renewed their romance.
During the Borg virus crisis she was used as a distraction by Director Brenna Covington of Starfleet Intelligence to shift away from Covington's real plans. Covington had claimed that there was a mole working in Starfleet providing technical secrets to the Orion Syndicate and assigned Libby to investigate. She soon realized that the evidence Covington provided did not add up and started investigating on her own. She was able to piece together Covington's overall plan of surgically transforming herself into a new Borg Queen. Realizing that she was in no position to stop Brenna Convington herself she covertly assisted the former senior staff of Voyager by calling herself Peregrine and communicating via untraceable messages.
While Harry Kim was lost in the Delta Quadrant she had a romantic relationship with her superior Deputy Director of Starfleet Intelligence Aidan Fletcher. She turned down Harry Kim's subsequent proposal of marriage, as she was unable to reveal her Intelligence activities. (VOY novels: Homecoming, The Farther Shore)
An alternate timeline version of Webber appeared in the episode "Non Sequitur".