Unofficial Fallout 4 Patch

The papyrus log error reported in #28401 explains why this happened.

For this to understand, one needs to know that the "Ness Story" consists of three more or less separate quests:
(1) the random encounter that spawns Ness
(2) DN123
(3) REAssaultSC01_DN123SkylanesAssault

The random encounter that spawns Ness [NB: she does not actually spawn but gets teleported to the encounter site from a holding cell] repeats until the player physically meets her and talks to her. After accepting her proposal, DN123 takes over (this is essentially a controller quest). The very first thing DN123 is supposed to do is to make sure that the random encounter trigger at the Skylane's site will start REAssaultSC01_DN123SkylanesAssault (instead of a randomly chosen attack) when the area loads up for the next time.

In your game however, something went wrong and REAssaultSC01_DN123SkylanesAssault did not start, hence the errors from ticket #28401 (they indicate that REAssaultSC01_DN123SkylanesAssault is not running although DN123 is assuming that it does, and trying to set a stage on that quest fails). Instead, the trigger started a generic assault. This broke the quest irreparably.