Here is one idea for how this story might go:
The origins story of Ratchet & Clank is becoming a very popular topic of discussion with the releases of the HD Trilogy bringing us those early adventures once again, a movie re-envisioning the first adventure, and even another game coming out on PS4 with a similar goal as the movie.
So why don't we do this for LBP2? Re-envision Ratchet & Clank meeting up, and their quest to take down their first villain. Little is known about the movie and PS4 games plot, but we do know there will be Nefarious. So here is my attempt at creating a story suitable for a couple of LBP2 levels.
Underlying plot: I'm going to go full-on unoriginal here, and actually use an unused story I came up with a few years ago… what? I'm feeling lazy! Anyway, basically it will all be much closer to the way LBP story levels are done, by having an underlying community link, (like MGS's level spammer, and the collector's stealing).
Everyone is aware that from time to time mysterious things happen for no apparent reason. And a LBP creator curator named Drek is experiencing some serious trouble making levels. He is a professional with Sackbot logic, and is known for breathing life into the little creatures. Well at least he would if if Moon wasn't playing up. Every time he tries to publish a level the level vanishes from his moon instead! Becoming enraged he refuses to let it rest. He comes up with a plan to actually steal other people's moons, and use them to publish his levels. But he goes overboard, and steals way too many moons, in the hopes of creating enough levels so that his Sackbots can be found in every player's inventory, and in every community level. He will be the greatest creator of all time!
But at the end of the day the real villain is Dr. Nefarious! Who sabotaged Drek's levels, knowing how he'd react so that he could take over LBP by flipping a switch to make all of Drek's Sackbots work for him. And with such a large army, he'd be unstoppable.
This seems like a big line of levels, but really we can compress it as much as we want. But the real question is weather we have:
Sackboy & Clank
Ratchet & Sackboy
or Ratchet, Clank and Sackboy
I'll explain them
Sackboy and Clank
Sackboy is running about in his latest level: Veldin, where he's created a cool new rocket ship he can use to visit other people's moons. Too bad he's unable to finish it off. Luckily one of Drek's not-so-evil Sackbots crash-lands in his level, searching for assistance. Clank explains it all to Sackboy, and before you know it we're off!
Ratchet & Sackboy
We start in one of Drek's Sackbot creation facilities. Sackboy is his latest creation. A perfectly normal Sackboy, but with a few hidden abilities (Like controlling other Sackbots with your 'mind'. So Sackboy escapes the facility via an inter-moon shuttle and crash lands on Ratchet's moon, where you help him with his ship so that the 2 of you can stop Drek (Use Infobot to explain it to Ratchet, because Sackboy can't speak)
Ratchet, Clank & Sackboy
Sackboy is helping Ratchet with his ship, by collecting parts scattered across Planet Veldin. Then a ship crashlands nearby. Ratchet asks you to check it out, and before you know it you've got a little robotic sidekick, Clank. You and Clank reprt back to Ratchet, and Clank explains the whole thing! As the 3 of you try to gather more info on where Drek's moon is you meet all sorts of characters, like Al, Helga, Qwark, the Rangers, the President, Skidd, and a Blarg Scientist (A friendly Sackbot of Drek's). Before finally getting to Drek's moon and blowing it up! But then you need to go through Nefariouses evil Sackbots to stop Nefarious in a final battle!
I like the 3rd option the most, and the levels could go as follows:
1. Cincematic - Intro Ratchet
2. Level - Help Ratchet, find Clank, and report back to Ratchet
3. Cincematic - Intro Clank, and reveal Drek's plan
4. Level - Explore Metropolis. There are 2 paths, one where Al gives Sackboy the Cape halfway through, and one where Helga gives Sackboy the Swingshot helfway through.
5. Level - The phoenix. The President has asked for some help, and you must fight through Drek's evil troops with your wall-kick ability. Eventually to make your way to the Bridge, where you save the president, who tells you of an expert who knows where to find Drek.
6. Level - On Aridia you find Skidd, who claims to be the expert, and gives you the Creatinator, which you use to find the real expert, one of Drek's Sackbots; a 'Blarg Scientist'. This guy tells you where to fins Drek.
7. Level and Boss - Drek's moon - Using some powerups you stop Drek's machines and eventually Drek himself.
8. Level - Drek's worst creation reveals himself as Dr. Nefarious. You must fight through the army to stop Nefarious!
9. Boss - You fight and destroy Nefarious and the Moon!
10. Cinematic - End.
If it's too long, then numbers 3, 5, 9 and 10 are disposable!
So this would be between 6 and 10 levels long, if you choose my option.