I am working on a quest but have to admit not having the first clue how to do it.

1. Go to NPC and speak to him.
2. He informs player of daughter missing. Ask to find her and return her to him
3. Go to docks and ask around. Meet second NPC. Agrees to take player to last location by boat.
4. Player goes into boat.
5, Time passes and player comes out of boat on to deck.
6. Player leaves and goes to location of temple.
7. Boat disappears and goes back to first location.
8. Player enters ruined temple and finds daughter with guards holed up under siege.
9. Player leaves temple with all four NPC's (all will follow player)
10. Player must cross land with NPC's and return to location of father
11. Quest ends, given cash.

Could someone give me a rough idea of how to do this. I appreciate it's complext so any help is appreciated.

That sounds similar to http://www.uesp.net/wiki/Oblivion:Caught_in_the_Hunt. Might want to dissect that quest. Take it in small chunks, watch where you put conditions and such, make sure it comes out logically.

You'll probably want a bit of http://www.uesp.net/wiki/Oblivion:The_Noble%27s_Daughter too, for the "take me home" part at the end. That's the only part that Caught in the Hunt doesn't have. In particular look at the AI packages for the participants.

And a small hint: if you have multiple followers, make the follow distances differ by at least 50, or they'll be tripping over each other all the time!