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The way you're "supposed" to do it, the way I think studios do it, is they create a big design document outlined everything that's going to be in the game from the outset, build that, and test it. Since I'm mostly just working by myself, I do things a bit differently.

First I get a concept of what kind of thing I want to make, such as "EarthBound characters explore haunted house (Andonuts Mansion)", or "Pop Star Debut as a JRPG (Octo Vinctum). I also try my ideas with my friend Mareeta to get some more input, then I start planning the general features I want to include. Example: Combat with Talents and words, visual novel segments, explore towns, etc. I also usually come up with the basic idea for the beginning, some middle events, and the end state. For Octo, it was "Sabrina leaves home to pursue her dreams", "meet friends and fight Synchronicity beasts", then finally "showdown with ultimate evil on the moon".

One big important step is to choose a game engine. For me, this has always been GameMaker. For what it is you want to make, I can give more recommendations. I also decide the art style for the game, for me limited to my and Mareeta's drawing abilities. Having a dedicated artist on the team is ideal, and you can always get free assets online too. I perfer using my own assets as much as possible.

Once I have a general idea of what I want to build, I just start building. I've made a lot of unfinished project and know how to code just about anything I need, so this is easy for me. If you haven't done a lot of coding before, it may be tougher to get started. The way I learned was by just trying to build things a bunch of times until I eventually found the best way to implement mechanics.

I first build the most important mechanics first, like the overworld player character, the most used menus and the combat system. The goal is to make the basic features so that it's easy as possible for you to add new content. As an example, all my RPG NPCs inherit code from a parent object so the only difference between individual NPCs is the line number (for dialogue), the sprite, and some AI/movement stuff. That way I can just place a new obj_npc_man2 in the room, give him a line of dialogue, and call it a day. 

A lot of my projects have died before reaching the end of this point. The few that have survived reach the point of me just adding more content from the existing systems until I have everything I want. I often get new ideas as am I'm working, which I'll try and implement to see if it makes the game better or worse. Blindly accepting new ideas into your game can be dangerous, as it can make your game way too complicated to work on if you don't control yourself. Trust your own judgement there.

The last step is to playtest, another topic on its own. Get other people to play your game as much as possible,  luxury I've virtually never had. A fresh set of eyes will help you see problems you can't.

I hope that helps. I tried to make my process as brief as I can, but I can go into more detail if necessary.