when I return to main menu, it keeps the game scene going even when I have returned. so when I hit play it keeps the progress from before I hit return. how do I fix this?

What game is this? Send me a link and I can take a look!

its paradiver, but I don't have the bug on the playable because this is a new problem from my recent edits to the game.

I'm assuming the menu is a seperate scene?
My usual command is SceneManager.LoadScene(0); (or whichever number scene you wish to load)

Another thing if things are being changed by a script, are the values assigned at the start or just updated as the script runs?

I honestly don't know how much difference the second one makes as I've never had the issue before, and haven't been at this very long (As in, i've tinkered through the years but never made any actual games until just over a week ago)

I think I'm going to just leave the game be. I don't want to ruin it.

Do you have to fix this? you could manually reset it as a quick fix. Since these are just for the challenge.

What I meant was, you can manually position the player at start, and clear the scene, and reset all of the score points. 

If it makes you feel happier about changing stuff, you could duplicate your project folder so that you have a working backup to revert to? I don't know if you do that already but I only figured it out a couple days ago :)

Also if you haven't already, try looking up "How to add a menu to my endless runner unity", or something similar that fits your issue, because although your game isn't what you generally think of when someone says endless runner, I reckon a lot of the concepts (and their code if you really need!) could very easily be applied to it