Cruzer gets sent to the shadow realm.

[Jamaar]

I was doing the rig attack mission for the Grim Jetters and went the infiltration approach using work coveralls to hack the sonar system and disable it. I returned to the ferry, talked to Cruzer, and left the rig. After I had made my way back to Port Ceto I spoke with captain grim and noticed Cruzer was not there, and looking at the quest log part of it still says to disable the turrets despite the sonar part of the quest being flagged as completed. I really am not sure what happened but I wonder if Cruzer just doesn't exist anymore and whether this will affect my gameplay in any way.

[harperfan7]

Recently tried out the third raid a few different ways and one time Cruzer was missing just like for you, though I didn't look at the journal. 

[Jamaar]

It turns out this only occurs when you join with Cruzer and then stealth/infiltrate the rig. Before I talked to the disguised pirate to go to the rig, I went there by myself and did the mission solo. After I returned to Captain Grim and talked to him, Cruzer actually appeared on the bridge of the destroyer. I even replayed a save and tried disabling the turrets using persuasion but no matter what the Eels turned hostile whenever I flipped the switch with or without convincing the guard to let me do so. If you plan on stealthing or infiltrating the rig go there yourself without joining Cruzer otherwise he'll disappear when you talk to Captain Grim again.