Evelyn discovered evidence linking a high level government official to the VX nerve gas terrorist attacks which occurred during Day 5. Evelyn had passed this information to former PresidentDavid Palmer, which eventually led to his death. Christopher Henderson, one of the masterminds of the conspiracy, discovered Evelyn had this evidence and kidnapped Amy around 9PM.
Amy was held captive until 11PM, when she was freed from her captors by CTU agent Jack Bauer, and David Palmer's brother, Wayne. Jack and Wayne secretly transported Amy and her injured mother to a motel for safety, but had to leave them unattended in the course of duty. Later on, Evelyn collapsed and Amy frantically called 911, allowing Henderson to track them down. Shortly after an EMS paramedic woke up Evelyn with smelling salts, Henderson barged into their room. He killed the two paramedics, and Amy screamed in fear.
Amy and Evelyn are not seen or heard from again after Henderson tracked them down. It is plausible (but not confirmed) that they were killed, since he was able to get the information out of Evelyn, and he was willing to sacrifice his own wife to ensure the safety of the conspiracy. It is also possible that Henderson let Amy (or both of them) live in exchange for Jack's location.