I have a group of PCs that are about to invade a large ship where they might encounter xenos, cultists, psykers or some combination of all 3, as part of a grand finale of sorts. Due to the situation up until now they have about 2 dozen special forces coming with them as support. The idea is they will make their way to the bridge to face off against a campaign nemesis.

In order to not bog down combat throughout the session(s), can anyone recommend a graceful way to get the player-allied NPCs to exit? I'm not sure if its best to just kill them all off randomly or if that would seem way too heavy handed?

Not necessarily just kill NPCs. You can create - and colorfully describe - a lot of situations where the faithful companions remain behind , covering&supporting the further movement of the PCs.

and to followup, while they are holding actions and support, that also allows the NPCs to be there if there is need for reinforcements for the final battles.

Maybe they are working their way through a different part of the ship with their own objective, which they have to complete so the PCs can complete theirs.

Maybe someone dies to save the PCs. That happened in a game where I was PC. A character who had gone through so much with the acolytes charged a strong daemon to give us a chance to escape. It was sad and we said we had to complete opur mission to honour this character.

Actually, you could have a lot of fun with this, especially if your game isn't deadly serious. You could have these special opps wear red shirts .

Let's say there are about 20 soldiers with you. Just create about 10 encounters in which 2 die during each encounter. Or even better, the death of a redshirt signals the start of the encounter.

WH40k ships are huge so you need to travel quite a distance to get to the big bad foozle anyway. Crawling through crawl spaces. Moving through tunnels in which plasma is being vented by the defenders. Fight through roadblocks. Cut through the tunnels and slide down to the ship's bottom (where the sludge and the creepy-crawlies are) and try to circumvent the main defences. Make your way through the ship's anti-boarding maze. Or have a bulkhead slam shut, cutting off some redshirts. The players have to open it in time while the redshirts are being slaughtered by something nasty. Do they even want to open the bulkhead or use the opportunity to put some distance between themselves and the big nasty?

And every time, at every encounter, one or two redshirts die. Pretty soon, they will realize few if any will make it and become morose or religious or even suicidal or trigger happy or just pissed etc. etc. etc.

Thanks so much for all the comments!

Thus far i've eliminated:

- 7 due to a warp beast attack
- 2 due to a failed fear test where they ran for their lives

15 left to assist the PCs while they fight 3 dark eldar scouts and see how deadly these xenos can be