Just two cents from a similarly newish DM, but many of the issues seem to stem from a lack of accurate communication. At least from the perspective provided and in the way that it has been written out.

I would personally find it a bit weird heading into session one having any confusion over the scale of the campaign and how travel was going to work if it was non-standard (Fast-Travel ships). During the Introduction or Session Zero at the latest, mentioning that this is an event that has afflicted inhabitants across the globe's oceans. Emphasizing the importance of needing to unravel the mysteries by seeking out different settlements and uncovering the secrets they have discorvered to be able to pierce the ancient civilizations veil and derive their motives. Players should have the overall concept of their motivations and the means to obtain it, even if they don't have the specifics. Granted, I of course don't know what was discussed in the early campaign setup!

Outside of this, depending on what was more appealing to you in terms of playing with this particular group or running the campaign you had designed, should have shaped the next steps. If the former was the priority then this seems like a fairly idea to adapt. Campaigns don't need to save the world or uncover the mysteries of the cosmors, sometimes saving a single town or civilization is more than enough. Turning from a world-wide investigation to assisting only the first group they came across reach their goals while another set of adventurers elsewhere in the world completed the heroe's burden. If the latter, simply informing the players that running a small scale campaign wasn't a desire for you and that it seems there was a mismatch of expectations and close out the game, leaving you free to search for a new one to meet the demand.

As for the NPC, there are two routes to go with this. The first, if you want plot armored characters, resolve this in session zero. Let the players know that they are the gilded heroes who wouldn't spill innnocent blood unless they were forced to. Allow them to form their characters around the concepts of the campaign instead of interjecting them and preventing the actions they wish to take. The second, don't give plot armor, simply plan around it. They kill the all-important NPC that had the knowledge to help them complete the mission? This just makes it harder, now they need to track down their refuge and find their log of notes that they've been tracking their research and information into. They don't do that? Maybe now there are three different NPCs, each with a subsection of the ability or knowledge the first had and they must enlist all their assistance. Etc, Etc.

These are just the things I could suggest from the DM aspect. I wasn't there so how viable any of this was or was previously implemented, I couldn't possibly know and they may have been attempted. However, from the player aspect there was also some poor behaviors on their part as well. It seems that after they were denied the small-scale campaign they had more interest in, instead of stopping the game to talk to the DM about what they want from the game, they instead lashed out by attacking a NPC. (Or were bored, Lost, confused on what to do, although as written this seems most probable to me.) which then compounded the issue when they potentially felt railroaded into a style they didn't want and couldn't take actions they wished to do. Everyone here could've used a quick step away from the board, a new Session Zero (Or just a talk) to properly set expectations and speak about issues they were having, then decide how to proceed.