That story = Awesome.
It hasn't even started though… there are plenty of twists and such stuff… like meeting Daxter (or Jaxter) and lets not forget about Dark Eco!
I can help you stay true to the J&D story, I've studied TPL very closely and know the ins and outs of eco and precursor tech!
Eg. The Precursors are said to have discovered Eco and learnt it's secrets allowing them to use it's power to craft the world (like gods) the myth could be stretched a little, and in reality they probably just learnt how Eco worked and the world already looked as it does in TPL (without humans though) however created strong metals (orange Precursor metal) and constructed large machines out of it. Spending years building up the planet to make it what it is.
Then there is the stuff with the Dark Makers and such stuff…
Anyway, I have come up with two ideas. Dak sets off as a young boy (maybe like 13 or something?) in Sandover who sets off to link the different Precursor worlds with the Teleporter Gates, running into each sage and their awesome worlds and elements along the way! Including Daxter who joins your group (Samos, Dak and Keira) however when Dak reaches the Yellow Sage he is told that there is a new member to the group of Sages; Gol (and Maia) who discovered a new eco type (do I need to explain this?) but Gol is being attacked by a great menace; a Lurker who has been touched by dark Eco (an experiment) this Lurker (you can name him) has an army of Dark Lurkers that you must fight through to save Gol. After saving Gol Samos warns him of the dangers of Dark Eco, but Gol assures Samos that with time he will learn it's ways and use it to 'recreate the world' though in such a light and friendly way that Samos trusts Go, and leaves him with the warning that he should never let it get to him… then as Samos, Dak, Jaxter and Keira walk off at the end Gol grins and his eyes go black.
The second is that Dak and Jaxter just defated Gol and Maia at the end of TPL but don't have the power cells required to open the gate. So they go to get the other cells required, but then the Silos burst when Dak gets back to Sandover to collect the final cells, and out from the Silos emerge a powerful Gol! The Precursors realise that something is very wrong, Dak was not supposed to miss any Cells, and there is a great issue, without the Metal Heads to take the Dark Eco in the Silos and use it to live long Metal Head lives, Gol has absorbed the Eco and become very powerful! With the land being transformed by Dark Eco Dak and Jaxter don't have much time and the Precursors present themselves (as holograms) to grant Dak Light Powers. Throughout the game Dak will get Light Powers and use them to destroy the Dark beasts across the land. Eventually leading back to Gol and Maia's former Citadel (now an elite fortress of darkness) to confront and destroy Gol and Maia once more (ending with the activation of the Rift Rider!)
And along the way Dak must get the Power cells back that he lost when the Silos exploded.
There two stories I came up with just now, use them if you want but if you don't want to it's all good, I just came up with them on the spot.
The first one was preety good and I may consider it, since my story of Dak visiting other video-game worlds sucks I may use it. The second one, altough it is preety good, it's kinda hard to do gameplay wise. Unless my mind comes up with something better than Video-Game cross-overs I'll stick with your first one.
I purposefully made them booth suitable for a game, though I'l admit the second would be very cinematic and difficult to do. The first one could be done using just dialogue, and no cinematics (makes it so much easier)
I would hate to take charge of the game your making, but perhaps we could share ideas as to how the game will play out? I don't know what the program your using is like so I can't really get that much of an understanding as to how the will work, I'm guessing a platformer game with fighting in 2D. First things first is you'll need Playable characters and NPCs. I would recommend creating Dak, Daxter (human) Samos, Keira, Gol, Maia, the Sages, and some Lurkers before creating levels.
I think that if you are going to do the first story you should break it into section like the first game, having Sandover, Rock Village, Lava Crater, and the Citadel. At the Citadel area (final area) the Yellow Sage should be met, near the end.
Of course these are mearly recommendations, and the locations can be changed as much as you wish, as it would really suck to not get to choose where Dak goes.
. And it will be on the old location, but the level design will be different. Oh man Daxter. What about a "Hey, wait for me" Daxter?
