Secretary has many major events and side quests. The main storyline - if you avoid all other content - is that your character gets a new job, and eventually gets turned into a sissy secretary. There isn't a strict "ending" but there is a point where you'll run out of new events and you'll just be left with going to work and being a good girl.
Although... isn't that what you want anyway?
These are the main checkpoints of the feminization process and how to get them to trigger. They're designed with 4 routes (or "styles") in mind but making a particular choice doesn't lock you into a specific route. Mixing them too much may get confusing or cause bugs, but should otherwise work.
Note on the warp system: At the beginning you're given the option to skip to different stages so you can get to new content without replaying huge sections. This is an experimental feature mostly used for testing, so it will often cause you to see certain scenes that happen earlier in the game and can cause other unexpected behaviors. Use at your own risk!
Forced - Your character is resistant to the changes, even a bit bratty. Secretly however, some part of them still wants it to happen. Follow this path by resisting all changes presented to you. This route goes faster than the others right now (v0.5.1)
Obedient - a.k.a. "Good Girl" - The character is adrift in life and has no self direction. So when someone in a position of authority makes a suggestion, they follow it without complaint. Follow this by doing what you're told, but no more than that.
Voluntary - The character is already into all these things on his own, and maybe isn't really a "he" to begin with. Either way, they take the initiative to try new things before being ordered to. To follow the voluntary path, you'll have to find a way to acquire new outfits and work up the willpower to wear them outside.
Greedy - Your character is broke and just wants to stop worrying about rent so they're looking for any chance to make more money. Capitalism makes people do some crazy things. Follow this by resisting changes until you see a way to make money.
The main events in the guide below are the main "checkpoints" on your path to becoming a sissy secretary. The minor events can happen in different ways, but won't affect your feminization style much. This guide doesn't cover every single choice you can make in the game, just the most important ones and things that may be unclear. The stages are just a way to keep track of what part of the story you're in, they don't directly affect side quests or other content. Those each have their own requirements regardless of which point of the "story" you're in.
The requirements are your requirements for morning inspection during that phase. Some paths may have a bit of overlap between stages, so the requirements are just listed here as a basic guide.
While most stats are fairly self-explanatory, willpower can be a bit more confusing. In general, willpower points are awarded for persevering through tough situations, or pushing yourself to do new things. Other times, trying new things will require you to spend a willpower point. Your maximum willpower goes up by increasing your smarts or stamina, but goes down as your sex obsession and submission stats increase. You can add to the max during certain story events.