At the moment version 3 is the new one out.
Everythingis backwards compatible but not forwards. So Characters from one, two and three will work in three, charcaters from 3 won't work in two and characters from 23 and three won't work in one. The same for mission and power disks packs.
There are two sides to the game.
Firstly There are missions (like the clear model in the center of the star wars packs) you can only play them with the relevant characters. So marvel missions need iron man, thor, black widow etc. Occasionally you can unlock crossovers in games. The missions really are the smallest part of the game, but the mission that comes in you starter pack are probably the bit you will spend most time on first.
Secondly there is the toy box. The toy box is vast and i can pretty much garentee you will never reach the end of it! Allowing for compatibility, you can play whatever characters you want and you can build your own levels, they can be as simple as plonking a few enemies down and fighting them to a fully themed level with games and logic links that you link yourself. Great way of looking at basic programming and game design
Then you can also download levels other online players have created or upload levels you have made for others to play. There is a fantastic you tube channel run by disney that sets build a level challenges and then shows off the best.(basically a great way of finding good user generated content.
Power disks sit under your character and change something. It might be the characters outfit, the sky and scenery, at tech, mode of transport.