PC Playstation 4 Xbox One X6-88 may not appear next to the player's quarters at the Institute, preventing the final objective from being completed.The quest will proceed normally once inside the cabin interior. To do so, simply do not speak to him and proceed to the cabin on top of the ship. It is possible to clear the area without the help of X6-88.Additionally, Curie dislikes reclaiming B5-92, yet she comments when asked that he "deserves this fate." Further along, Danse "hates" refusing Gabriel's bribe or electing to take his loot by force, yet his spoken responses are "A wise choice, soldier," and "This is going to be a pleasure," respectively. For example, Nick Valentine "loves" saying it would be more humane to kill Gabriel than use the recall code, but states "I think you and I got real different definitions of 'humane'" which implies he should not like this choice. There appears to be a disconnection between the affinity changes generated and the actually spoken responses, for many of the companions.
If this happens, proceed to Gabriel: X6-88 will teleport to the Sole Survivor upon entering the captain's cabin at the top of the ship, and the quest will progress from there. Since X6-88 is essential, he cannot lose the fight but will continue to fight ad infinitum. The Brotherhood members will not be hostile to the Sole Survivor unless they are already an enemy of the Brotherhood of Steel.
There are a couple of persuasion checks that give extra choices like the password for the Master locked terminal that can open a nearby safe.
Using the synth's factory reset code will disable Gabriel and keep the fight limited to a few raiders. On reaching the top of the ship Gabriel will initiate conversation, and no matter what, a fight will break out. Upon entering the cabin, the courser companion, X6-88 will initiate a conversation and provide Gabriel's recall code. Once he is collected, fight along with the network of ships until the target is reached. There will be a courser companion at Nahant Wharf or the shore northeast of Nordhagen Beach, depending on from which direction the player comes, who needs to be collected first. Speak with Father about the Institute, he will request help dealing with a renegade synth turned raider at Libertalia.