I'm clueless how to make a clever plot that's consistent, and say leads up to fighting a boss or something like that, while playing with an extremely inexperienced player.
You're the GM. Your job is not to write the plot. Your job is to create a
situation, then allow the players to interact with it. Players write plots, not GMs.
Example of how to NOT think about it:The players start at Twilight's library. They're reading a book with Twilight at the table when Spike comes rushing in, visibly distraught. He goes straight to Twilight and loudly explains that somebody broke into Carousel Boutique through the back entrance and stole a of gems. The player will go to investigate, where they'll discover hair at the scene of the crime. After taking samples and investigating they'll realize that these are diamond dog hairs. Twilight, Rarity and Spike all remember when Rarity was kidnapped, and they'll inform the player of where the diamond dog lair is outside of town. The players will go investigate, immediately discovering a few dropped gems alongside a set of dog tracks. Upon arriving at the lair, they encounter a lone diamond dog, who, terrified at having been caught, explains that he's the runt of the litter and too small to dig for gems. So the bigger diamond dogs threatened to beat him up if he didn't find a way to get some, so so reluctantly stole the gems in order to win acceptance from his peers. Hearing this, the players will offer to be his friend and give him their acceptance. He'll be overjoyed, and accept. The players will then write a letter to Princess Celestia explaining how they've learned the value of acceptance, listening, and giving people a chance.
The above is complete and absolute suicide for a GM, because you're assumed a long and specific string of events, every step of which depends on the players doing exactly what you expect them to. Players never do what you expect. What if the see the hair and ignore it, concluding that it belongs to Opalescence? Then suddenly you have Rarity becoming eh voice of the GM, suggesting that they go talk to Twilight. What happens if they don't go back to the library after discovering the hair? What happens if the figure out it's a diamond dog hair so instead of going to investigate, they decide to write a letter to Celestia requesting the intervention of the royal guard? Then, once again...you end up having Twilight be the voice of the GM streamlining them into the action you expect. What if they ask Twilight to come with, because they don't want to get kidnapped by diamond dogs? That's a very reasonable objection. They're fillies. Do you really expect them to go off on their own? So what then? Do you have Twilight say no, they can take care of it? That breaks suspension of disbelief. Or do you have Twilight tag along? That reduces our players into irrelevant tagalongs while they watch an npc do everything.
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Example of how to think about it:There is a diamond dog runt who is stealing gems from Rarity because he's not strong enough to dig for them, and has been threatened or manipulated by his peers to get gems one way or another.
DONE.
Exact same scenario, but is one case you're planning one the players are "supposed to" do, whereas in the other, you're not. Being a gamemaster is not simply telling a story to a passive audience, and being a player is not simply listening to the GM then saying your lines when it's your turn.
To be a good GM, create
situations. Do
not create solutions. Let your players do what they will. Don't even assume that they'll resolve the situation you hand them. They might want to do something totally else.
how to make a clever plot that's consistent
The easiest way to create absolute plot consistency is to NOT create a plot. Players write plots. GMs write scenarios. Create a situation and allow the players to discover it. Then detach yourself from any particular outcome and become the voice of your world, reacting to the players actions. Your only goal is to ensure that everyone has a good time. It's not your job to create solutions, it's not your job to resolve anything. Let the players play the game.
and say leads up to fighting a boss
Perfect example of what not to do. Oh...by all means have a boss fight
available, if the players should happen to go somewhere where there might plausibly be a boss to fight. But do NOT "lead" the players to that fight. Let them do what they want.
while playing with an extremely inexperienced player.
Teach her that it's an open world and that she can do whatever she wants. She might surprise you. She might ignore the Botique and get on the train for Canterlot. And if she does, that's ok. Maybe she doesn't want to talk to diamond dogs. And if she doesn't, all that time you spent creating that long and complicated "plot" with your preconceived notions about how it would resolve was a waste of time.
Build a world and let them play in it. Don't create a story and walk them through it.
Please help.
Do you have specific questions?