Your PCs are acting as vigilantes, and as such that should come with the consequence of murdering someone.

I can think of a few ways to handle this off the top of my head:

1. Have the local authorities (ex: town guards, military, city watch) come after them and launch a full investigation into the murder of this NPC


2. Have the rest of his gang find out that the PCs murdered their boss. Maybe there was someone in that gang looking to have the Boss killed so they could rise to power.


3. Have the rest of his gang go a on quest to attempt to resurrect him using relics that the PCs need to collect before they do.

Either way, you can use this as a way to change the story.

I agree with adapt and move on, but an alternative is to

look at what the boss has up their sleeve to prevent this

An intelligent enemy won't put themselves into a situation they don't think they can escape from, so maybe he is a magic user and "You reach for your dagger and as you strike the captive vanishes, he reappears seconds later in the corridor, turns and runs" (IE: Casts Misty Step as a reaction).

Maybe he is a hardy barbarian and "You push the dagger into his chest which resists like it was made of steel! A small dribble of blood runs out where you would expect a flood. Suddenly his muscles tense and he breaks free of his bonds!" (IE: Bear totem resistance to non-magical piercing, followed by raging and gaining advantage on strength checks to break the ropes / manacles).

It might be too late for you to do this now, but equally if your PC's were taken captive I don't think they would like to be killed like chumps, so can probably understand the NPC's not going out this way. Your boss would still be unarmed, unarmoured and at a serious disadvantage, but at least he would have his HP and actions to make his escape.

Serial outcomes to BBEG's execution: Revenant and/or Deputy

If you look into the Monster Manual entry for Revenant, you'll find this opener:

A revenant forms from the soul of a mortal who met a cruel and undeserving fate.

Whether the BBEG met a fate as characterized there is up to you as DM to decide, but as the party continues with their adventure they will eventually discover that they are being tracked by a Revenant. Or, the Revenant will make an entrance at a key moment with the stabber squarely in his sights.

Meanwhile, since the boss has been taken out ...

BBEG's deputy takes over

You don't miss a beat in the adventure. Your BBEG's right hand man/woman was looking into {something} concerning their criminal/evil/nefarious enterprise. As with various criminal organizations, once the top dog is gone Number Two takes the reins. Granted, you can let some time pass as this equally nasty opponent consolidates power within the bad guy group, but it's not that hard to drop hints that the bad things the BBEG's people were up to are still going on, or begin to go on again, with a slight change in style. (A different sign or letter is carved into the foreheads of assassinated foes of the organization, for example ...)

You can combine both of the above if you think it will fit the challenge and narrative for your party. Not only did Number Two take over (who now has an eye on how deadly the party is, and how ruthless the PC's are) but also the Revenant makes a grand entrance at a critical point.

Improvise, Overcome, Adapt. Gunny Highway's guidance applies to DMs as well as to Marines.

If it hasn't happened yet, you can retcon.

As a GM, you have a "spoken" or "unspoken" agreement with the players. You set challenges, they solve them, your world is consistent and they have agency -- their actions matter. So if they defeated the Big Bad through quick thinking and a few lucky die rolls, they deserve a reward.

On the other hand, you are free to change any element of the game that hasn't happened "on stage" yet. You are not required to make a plan before the campaign starts and to stick to it, no matter what. Some options how to cheat and adapt:

• Reorganize the "chain of command" of the NPCs. The slain warrior was only the second-in-command, and you introduce a new Evil Overlord. Either this new boss is weaker than the old one, or the players are rewarded in some other way for their success.


• The slain warrior was the Big Bad, but with his disappearance the former second-in-command makes a move. Again the new boss is not quite as capable as the old one.
  
  
  
  
  • As a variant, the Big Bad's conspiracy comes apart and new, different adventures happen. Send the players to secure the magic items in the slain warrior's arsenal, fighting a hundred brushfires rather than a big fight.
  
  
  
  


• If that is consistent with the information from the interrogation, decide that the slain warrior never was the Big Bad after all. He was a third party in the conflict, trying to profit from the mayhem in some way. That explains why he knew things, and it doesn't retcon him into an innocent.

Think through the clues that were handed out so far. Come up with a "new truth" consistent will all those clues. The slain warrior will be somewhere, but not necessarily on top of the pyramid.

Side note, as a GM you are allowed to cheat even in combat as long as you keep faith with the players. If cause-and-effect principles are violated, it follows the narrative logic. You deliver a fun challenge, they solve it. The actions of the NPCs affect the setting, and so do the actions of the PCs.

I would think it would be easier to have the slain NPC a doppleganger or simulacrum as opposed to the actual boss. This keeps the story line in place and will have a shocking effect on the PC's when they finally confront this boss. On a side note, what if any repercussions will happen to the PC that actually killed the NPC (does his alignment allow said action.) It's been a while since I've gamed, but depending on alignment there is usually something that happens if the PC acted against his alignment.

This kind of question may be a test in overall GM flexibility. One of the problems I've noticed in longer campaigns is maintaining GM power and flexibility in relation to the story and players. Games like D&D are designed in a way that reflects caution on the side of the developers. Over most other elements of the game, hard mechanics and rules systems are put in place to restrict the GM in an effort to prevent the GM from having too much power over the players. In some cases, this is important; some GMs might have a tendency to push the story in a linear direction in order to follow a pre-established narrative, breaking your realism and taking away the players' free will. However, these restrictive systems often allow for the rise of equally disastrous player abuse, rules-lawyering and rule exploitation. This balancing gives both positive and negative power to both the Gm and the players, and unfortunately might create situations in which the DM and players are in direct conflict. If you choose to, you can always continue to use these systems for their familiarity, preference, or providing balance for an unstable group. In this case, the best thing you can do is become more flexible, design your plot only a few sessions ahead, or create your narrative in a way that locks the finale and all of its elements in a steel fortress of GM fiat and plot armor.

However, there is always another solution to be found, if you are willing to change your mindset.

In what I would assume is the opinion of most roleplayers, the GM and the players should have an equal amount of power to influence the plot and narrative, with an exception being games oriented towards horror or hyper-realism. However, IMHO many people are missing the necessary second part of this opinion, which is that the GM and players collaborate to create a story for the purpose of fun and entertainment. For this reason, I believe that a plot should never be decided without the influence of the players, and yet it always should. Please bear with my explanation here, but if you've ever played or ran a game of Paranoia you might know what I'm talking about.

In Paranoia, most games go for a comedic tone with a lot of black humor and brutality, and thus end up as one-shots. In this kind of scenario, there are only two sure phases of the plot which occur with little agency on the players' part--- the briefing and the debriefing. Sure, the GM might have an idea for an antagonist or mission, but this can be derailed at any time through the normal course of player interactions. Especially in the context of Paranoia, the players themselves may cause enough necessary conflict to complete a game without ever having reached the official "start". This requires a great level of flexibility and compromise on the part of the GM, giving the players a huge amount of agency.

At the same time, the GM is given absolute power over the players along with the responsibility of using this power wisely. The GM can discard all of the rules and fudge all of the dice, making up a story and universe as the players progress. GM fiat and plot armor must be used wisely, but provide a conclusive response to the players who insist on rules-lawyering or ending your narrative and conflict in an underwhelming fashion. From another perspective, the GM also has the chance to ignore the dice in the favor of the collaborative narrative--that is, what the players have provided to create the story. If your player attempts to perform a ridiculous or nigh-impossible action to end an encounter in a satisfying or comedic way, don't let the dice get in the way of your group's enjoyment, just roll with it. As a GM, you have the license to use your power in either of these ways to create an enjoyable session.

From all of this, the most important thing to remember is to create a fun, working narrative. In your situation, I might echo some of the other answers and let the action go through, bringing with it the consequences of a power vacuum in the underworld. However, not knowing the exact circumstances of your table, I would just say to do whatever you think would benefit the story and the group the most.