Since you write stories often I'm guessing your problem is that you are coming up with plenty of ideas but don't know how to work them into the game.
First you want to plan out the framework of the story, like you would if you were writing a book. Once you've worked out who the characters are and where they are going it gets slightly different: think about the different places your characters visit, what would be fun to do there? What things could the player learn?
When making an educational game you have to be careful not to shoehorn in tedious tasks that don't make sense in context, if you want to teach something specific make sure it works in context. For example, if you join a pirate ship as the cabin boy and are tasked with pouring the rum for the pirates, the game shouldn't ask you to get out a measuring jug and divide it exactly between the pirates (I don't think the pirates would be too pleased having to wait for their rum to be measured!), so maybe the Captain could ask you "Ey me lil' lad! Yer a clevir sort, tell us ow many days rum we 'ave lef. We don' wansa run oot a rum now do we!", Then you could ask how much each pirates drinks a day (or just be given a list) and you work out how many days the rum will last.
Name Bottles O' Rum per day
Cap'n Knotbeard 3
Old Jim Baggar 1
"Glass-Eye" McGrew 4
"Poncy" Tim ½
Lenny Coates 2
Kalunga 2
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TOTAL 12½ bottles o' rum per day
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Bottles o' Rum in Storage 53
53 ÷ 12½ = 4.24 days worth of rum left
"Only four days‽", cried Captain Knotbeard, "but we're five days from land m'lad, and a pirate can't sail wi' no rum in 'is tum!"
How can you make the rum last for five days? (If "Glass-Eye" and the Captain each drink one fewer bottles per day the entire crew will have enough rum to last an extra day at sea.)
So you see the little tasks and games can be steered by the overarching storyline, whereas the rough plan would have been: they sail from A→B, now we've thrown in this rum fiasco half way through that the player has to solve so that they make it all the way to port B, and then we refer back to the story plan to see what happens after they reach port B and we repeat the process of finding things to do and problems to solve in the next part of the story.
I really like the idea that the kid got his place on board by showing he has some useful skills that the pirates lack, like maths in my example. When the pirates have a problem they can't solve with brute force they ask the "lil' lad" for help. He could do all sorts of things like navigating, reading (the pirates are illiterate), using treasure maps and sharing out the treasure, etc.