This Friday I'm running my L5R game with only 50% of the players. It's been a rule of mine since the game started that if I have 3 players I'll run, and with 3 players ready to go and wanting to game that is exactly what we're going to do. However, it does bring up some problems. The game is currently at a spot where decisions and character growth needs to happen. In particular, two of the PCs who are going to miss the session need to have some stuff happen before the main plot can begin. Still, I'm not too worried about that because it can be handled. How? To find out you need to read on past the break.
Small Groups Can Be A Blessing
It isn't uncommon for GMs to dread running sessoins when they're multiple players down, but it can be a blessing. For one thing, the smaller number of people at the table makes it easier to focus on those characters and their players. This means that if someone normally plays wall flower you can bring them in to the action with greater ease. It also means that if someone likes to hog the limelight that you can let them have more spotlight time without actually hurting the game. There are a lot of advantages to being a few players down beyond that too: the session generally ends up more focused, combat goes faster, and - best of all - it becomes easier to give NPCs some face time.
Adding Depth To NPCs
If nothing else a session when you're a few players down is a great time to give more depth to important NPCs. With less players there is more chance for interaction to happen on a PC->NPC level. The last time we were down a couple players in my game, working quickly, I was able to give some basic personality to almost every NPC in the area the PCs are currently encamped, and go a bit further in depth with several other NPCs to give them some real depth and flavor. This isn't something that could be easily accomplished with a full table of 6 PCs because every PC just adds so much more going on at one time that you quickly run into the choice of adding fluff to make on person's experience that much richer, or moving on to the betterment of all.
Personal Goals and Side Stories
Just as a couple missing players give a chance to add depth to NPCs it also gives a chance to add depth to the PCs themselves and the world in general. If the main plot can't move forward too much, you can always do side stories and show different angles on what is going on.
This benefits the people who show up. If not done carefully it can benefit them a whole bunch. However, I would also posit that that is the benefit of being the player who shows up to all the sessions. You get more chances to be involved, and more chances to thus become an integral part of the story. Not to the detriment of other players, but still to the enrichment of the players who are there.
Or Screw It, Do Something Huge
Alternatively you can just say "screw it" and do something huge. Some big and monumental. Something that rocks the game to the core and leaves people staggered. Generally you want all your players there for these momentous occasions, but sometimes it is better to have the small group of PCs. Why? Well it does two things for you:
First, these big momentous occasions and set pieces often include large mechanics heavy portions of the game, and less players means those portions can go faster making everything easier to keep under control.
Second, doing this on occasion helps give a sense that the world doesn't wait on the PCs to be ready and available for the big events. For this one to work though you need a reason for the PCs who aren't around in person to also not be around in character.