Again, it's going to depend on HOW your story branches. There's not really one answer to that. However, I can't really see any limitations being set by the program in terms of what you can deliver with a branching story.
Does your story branch by choices made? There's an option to have players make choices and set different events based on the choice.
Are the branches determined by some sort of hidden 'stat' you gain? Like a moral system, where good choices branch you one way and bad choices branch you another based on a cumulative value? You'll use variables and conditional branches.
Does an early choice effect game play later on? Probably a switch triggered by each choice. (or storing a variable at a different number based on each choice)
Does your story branch based on what you equip? Based on how fast you complete certain events? Based on how many of an enemy you defeat. Based on choosing to defeat enemies or not. Based on what time of day it is in the game. Based on what flavour of ice cream you say is your favourite.
Are there events that happen no matter what story branch you're on?
Are there events that can only be seen on one branch but not others?
Are there events seen on 50% of the branches and a different event on the other half?
Like... it's hard to say "Here's how you do THIS" when you aren't asking for a specific THIS. I could tell you how I'd handle my own branching stories, but that's not going to be very helpful.
No matter what though, I suggest familiarizing yourself with conditional branches, what conditions they can handle. Variables and switches. and the player Choice. (and possibly labels)
Most of which are quite aptly in the Game Progression and Flow Control second of the Event Commands. Show Choices is chilling up in the Message section there. There's 4 pages worth of conditional branch settings, they should give you a good idea of the most basic branches you have power over. But using switches and variables, there's honestly not much, if anything, you can't work around a way to control. (But again, no one here can tell you the best way to do something without knowing specifically what you're trying to do.)