Neelix is accidently killed by a protomatter discharge on an away mission  and then "reactivated" by Seven's Borg nanoprobes. He finds himself in a deep existential and spiritual crisis, questioning his faith and the meaning of his existence,

Seven of Nine discovers an ancient subspace relay network that extends to the Alpha Quadrant. They can send the Doctor through to a Federation ship at the other end, the experimental U.S.S. Prometheus, only to discover that Romulans have taken it over.