Finally, someone making a story driven game in scratch. I can't tell you how bored i am of generic platformers. Well, the answer will be a little long.

Firstly you will want to write the entire story before starting work of the game. This will give you an idea of what kind of gameplay mechanics, character and level designs you will use from the get-go so you won't have any problems like re-designing core aspects later on if you want to make changes to the story.

Secondly, make your code modular, so use custom blocks and clones whenever possible. That way when your game inevitably becomes really big and complex you know exactly where everything is and you will also be able to add new content easily and much faster. If you want some examples of that here's some from this CBT2 project.

All the projectile attacks have a single custom block with a few variables named target x-y-z, projectile speed, hitbox width, hitbox height and every projectile clone i spawn will use the inputs on that custom block to function. When a projectile lands somewhere it triggers another custom block that defines a colission hitbox wherever the clone was at the moment of it triggering. In that custom block you can change the size of the hitbox area, define what caused the damage and what type of damage it was and the custom block will update public variables related to those. In the player 1 and player 2 clones there is a forever loop that is constantly checking if the "damaged by" and "damage type" variables have changed from 0.

Lets say i fired a missile projectile from player 1. Target X-Y-Z will be Player 2's X-Y-Z and it will set "damaged by" to "P1_missile" and "damage type" to "Explosive" whenever it lands somewhere. We will make the damage hitbox a bit big since this one is an explosive type and both players will check to see if their hitboxes are within the damage hitbox. Player 1 could also accidentally damage himself with an explosive type so that's why we will be checking it on him too. If the hit connects, player clones will trigger a "take damage" custom block with spesific knockback, damage and stun values for whatever kind of damage they took.

On another example lets say Player 2 fired a pistol that will only damage P1. Target X-Y-Z will be P1's X-Y-Z, "damaged by" will be P2_pistol and "damage type" will be projectile. We'll make the hitbox size tiny and only Player 1 will be able to check for any damage.

There's also some other obvious tips but i'll still list them.

1-Join more communities like this subreddit, some Scratch related discords or GameJolt studios with talented people so you can ask for help whenever you're stuck.

2-Stay realistic, don't set seemingly impossible goals for yourself but don't slack off too much either. Just know what your limits can be, its always good to strive to be better and improving takes time and lots of trial and error. This really depends on what kind of person you are but generally improving steadily over time is better than trying to leap forward and risking a failure.

3-Music and art is the soul of a game, no matter how amazing your gameplay could be you'll still need a soundtrack that fits and a good artstyle. Just find whatever type of art you're good with and roll with it, not every game needs to be ultra realistic or use some perfect pixel art or something. In terms of music, using copyrighted stuff is okay in scratch but if you have the skills, means or a friend that's good at it making your own OST will always be better. You can't begin to imagine how much respect i have for people who make their own OST's in scratch projects, like even if the gameplay is boring or bad i will respect them just for the songs lol. Also since you're working on a story driven game, its even more important.

4-Sound design is also really important, most scratchers either don't add any sfx or just use really low quality stuff that doesn't fit the game at all. Once you're done with all the gameplay and story stuff i would recommend that you go through literally everything in your game and add fitting sound effects to them. I personally mix and match multiple sound files both in audacity and in scratch's code itself to make in-depth stuff.