The lytic phage ICP1 is engaged in an evolutionary arms race with its host Vibrio cholerae. ICP1 infection is specifically blocked by an anti-phage genomic island in V. cholerae named the Phage Inducible Chromosomal Island-Like Element (PLE). Infection of PLE+ cells by ICP1 is abortive. PLE+ cells infected with ICP1 die without producing phage; however, the mechanism(s) underlying interference of phage production are not known. To elucidate how the PLE interferes with ICP1 infection, we performed RNA-seq analysis on PLE+ and PLE- V. cholerae throughout the course of ICP1 infection. Differential expression analysis revealed temporal changes in the relative expression of ICP1 and PLE genes. Within 6 minutes of infection, more than 60% of transcripts mapped to the ICP1 genome in both PLE+ and PLE- samples, indicating that the phage rapidly takes over the cell. ICP1 expresses many putative nucleotide metabolism genes during early infection. As infection progresses, ICP1 expression is enriched in clusters that contain predicted structural genes. Genes encoded by the PLE are transcribed at relatively low levels in uninfected samples. Infection with ICP1 stimulates transcription of PLE encoded genes, with 10% of total transcripts in the cell mapping to the PLE at 12 minutes post infection. Operons within the PLE are expressed in a temporal pattern, suggesting expression of certain PLE genes is timed to interfere with specific phases of infection. Information obtained through these experiments elucidates potential mechanisms by which the PLE interferes with ICP1 infection.