My sessions vary between 2 and 5 players, usually. The fewer I have the more smoothly the session goes, but more people leads to more potential fun and ways of doing things. My players all started out with the premise that they were on the same island to locate some Matoran researchers. Then they got caught up in Skakdi and Dark Hunter plots, which led them to stay and fix things (most of them are Toa) even after finding the Matoran.
I have just let things evolve based on how the characters act, really. For the first session I had planned to introduce a villain and a mini-dungeon, but because the players never went in that direction I just quietly ignored the potential dungeon and had the villain encounter them on the road instead.
Players usually follow whatever plot tracks that appear to be useful or relevant to their interests. If containing Rahi seems like busy work with no real benefit, characters who mostly look after themselves will not do it.
If it seems like something they would not do, you need to either provide a real incentive (such as offering them a large payment, hinting at something more important than Rahi in the same area, having a villain force them to flee to that area, and so on) or you should offer more alternatives. It helps to plan out two or three potential things that could be done that are plot-relevant, and then plan out three or more leads to each of those things.
Example: Let's say the main plot involves discovering Karzahni and what's going on there. However, the main characters don't know this yet. Potential ways of getting on track towards Karzahni: Following a map, being told to go there by an Order of Mata Nui agent, tracking it down manually, and so on. Potential leads for each of these are finding the map carved on a wall, meeting a being from Karzahni or an Order agent, getting involved with other beings who have ties to either of them, and so on.
You can put relevant NPCs anywhere. They could be traveling, they could hire the main characters to do another job and then letting a secret slip, they could steal from the players or cause other things to happen that makes the player dead set on tracking them down regardless of any greater plot. Items - like mysterious maps - can also be placed in locations where they would appear significant. Someone could have had a vision of a place and drawn a sketch of it. Someone could be carrying orders and a map on their person. Someone could be discovered dead or locked in combat with evil minions that point to something big happening.
In your particular case, the Rahi in the Archives could have escaped because they were released as a distraction by villains, or they could be incidental but have now destroyed a wall leading to a previously closed-off tunnel. The missing Matoran could have been carrying something important that the players will need. He or she could also be in hiding thanks to villains, or maybe they are found already captured. The Turaga's staff may not be important per se, but completing the quest could earn him/her as a trusting ally and plot exposition machine. The staff could also be found next to a sunken vessel that contains more secrets and plot-relevant stuff.
If you want to be extra sneaky as a DM (never tell your players exactly what you are doing, though, it kills the magic) you can plan a single item/villain/plot hook and then place it wherever the players choose to go - no matter if that is in the Archives, on a rescue mission, or at the bottom of the bay. Just don't do obvious cheats like forcing a fight with a lava monster even after the players expresses their intent to avoid the lava area completely; that also kills the magic by being too obvious.
If you feel like it, you can even tie them all together in the end: You find the Matoran besieged by Rahi in the archives, or perhaps some Rahi have escaped into the bay and gathered around the glowing Turaga staff...
Also, don't be afraid to take your game in an entirely new direction. My Dark Hunters were meant to be a band of dangerous villains that could not be fought head-on. The players took them down with a few lucky roll of the dice, fast-forwarding the plot immensely and removing that group of Dark Hunters as a threat. The players then stole their ship and everything on it.