It's the Lilith-class cruiser. Fortunately, the Ignatius is unlikely to be destroyed by it, so that is not a major issue.
I just finished this. Wow, the last two missions were intense. A few minor issues, though. In the second-to-last mission, the Vasudan bombers are loaded with rockeyes instead of bombs (and with Prometheus-retrofits instead of decent weapons) as the default. In the last mission, if you fail the mission you get the same debriefing as if you had jumped out without permission. Also, I think there's no voice for some of the Cypher's lines in the second-to-last mission (when it is warping out against orders). Is this because they were not recorded, or have they been accidentally left out?