Good question! And one every GM has to deal with from time to time I would think. I'd probably pick one or two of these:
Keep the pace. Part of your story revolves around urgency. Let them feel stressed out, make your encounters heave for breath, more so the closer the party gets to the final boss fight. Try to make them feel guilty for even the slightest pause, thorough searching etc.
Help them recover. Let the PCs discover an old and forgotten crate with a nearly empty healing wand, some crumbling restoration scrolls and a six-pack of useful potions with faded labels.
Surprise the badguys. Villains also need to deal with changing schedules.
- An important ritual component is lost or spilled on the floor during preparation and a minion is dispatched to the nearest town to procure more.
- A pair of blundering ogres accidentally discover the villains hideout and must be dealt with, depleting resources.
- A cloudy night sky diminishes moon power, so the ritual is postponed for a day or two until weather clears up.
- The players can mess up the villains schedule. Give them a chance to funnel a swarm of dire bats into the villains part of the dungeon, thus creating havoc and buying time.
I thought about making up an excuse to talk to all players in the
bathroom during stuff like the assassination example above so everyone
will be suspicious of each other but it sounds like too much hurdle.
Unfortunately, that's your answer.
Metagaming in this case isn't going to be deliberate, but it's going to be hard to avoid. If you constantly talk to one player and one player only, even perfectly honest players trying not to metagame are going to have a difficult time not seeing suspicious activity in anything that one player does. It's human nature. The biggest danger of it is that you give a metagaming speech and the players over-compensate by ignoring suspicious activity so to avoid the perception of metagaming.
The only way to avoid it is to either not talk to that player so often at sessions (by talking between sessions and letting the player improv as needed during sessions), or by talking to everyone so they have no reason to suspect any one person over another.
Example from my campaign
I recently ran a session with my players that was a peace negotiation. Everybody was playing an ambassador for one city (or nation), except one (he was playing his own character, as the host of the session). Every nation wanted something out of the negotiation. One of them wanted to see the whole thing fail. In order to ensure that nobody knew who that person was, I wrote half-page notes for every single player and handed them out at the start of the session.
The troublemaker knew who he was (because his note said so), but everybody had notes so nobody knew who was getting different instructions from everyone else.
Is that more work? Yes, absolutely. It was a lot of work. But it was a big success.
Other Tricks
If everybody has a phone or tablet at the table, you can exchange chat messages. If you do it rarely enough, it won't be overly noticeable. Doing it too frequently will make it obvious who you're talking to.
If you have one player come early, you can talk to that player before anybody else shows up. People don't arrive at the same time for games typically, so that's not overly suspicious.
You can hand the relevant player a note at the table with important information, at the time. But again, you'll have to do this with every player from time to time so it seems normal. I've done this with cases where one party member notices something odd that they might not want to share right away (like if only they hear a weird noise or think someone's lying).
Best Answer
Truths to Work Into A Solution:
Result: I would play it out, but alternate spotlight time with the rest of the group, giving them more.
The other players are doing something while this PC is in their own world, right? Cut back to them and have them do whatever (with a sharp eye against the metagaming of "Uh, I suddenly decide to go for a run to find Julio"). Give them plenty of time. Then cut back to the combat for a couple rounds, and back.
This has the result of being fair to the solo combatant (and really, shouldn't D&D let people have solo combats from time to time?) and lets the others have equal spotlight time. Giving them a bit more helps dissuade him from doing this if he just wants attention.
Although, does he fade into the back in group situations? It may be a fair allocation of spotlight time already. I know sometimes I get frustrated when I am playing a PC who wants to do solo combats, honorably challenge a specific foe, or whatnot and my party is always kill-stealing.
I had a situation like this in my Reavers campaign recently. The monk went in and fought a whole installation of pirates without the rest of the party. On the one hand, he got beaten and captured, but on the other hand, he killed half the pirates so that when the rest of the PCs came they could mop up more easily (though he did then get used as a hostage...). The story outcome was entertaining enough, and I studiously swapped time back and forth between him and the others, so all was well in our eyes.
Also, there's only so long it could take, right, if it's a sure-lose situation? If it goes on very long, then by definition they have a chance to pull it out, escape, etc.
Oh, one other suggestion I've used from time to time - give the PCs some of the bad guys to play. This reduces your work, gives them something to do, and makes the opposition a lot more effective.