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.