Branching
Branching is the process by which a visual novel's story might proceed in one of several directions. The player's actions determine which branch or path the story takes. These decisions can take the form of explicit options presented to the player (even if it's not totally clear which option will lead to which path), but they may also be the result of multiple decisions over time, or even other methods such as the player's performance in a minigame.
Flags
A flag is an instance of a noteworthy condition/action being taken by a player that is recorded and saved as part of an instance of a game. Flags (often in multiples) are used to determine the various outcomes of events based on prior actions taken, and may have 2 or more states. A flag that, once triggered, eventually and inevitably leads to the player character or supporting character’s death is called a death flag. Telltale’s famous “Clementine will remember this.” notifications are an example of a tripped flag being overtly stated to a player.
Routes
A route is a distinct story in a branching narrative that is from a significantly different perspective or contains significantly different content than other branches. A route focused on a character(s) is a character route and is referred to by the name of the character(s) they’re revolving around. A route that is considered the canon route that is taken forward in sequels or other media is known as the True route. A section of a story before any major branches is called the Common Route. A route that is cut short or ends unfavorably for the protagonist and supporting characters is often called a bad end or bad route.
Flowcharts
A flowchart is (in general terms) a graphical representation of a workflow or process using symbols and arrows or connecting lines to depict the sequence of events. In the terms of a visual novel, a flowchart is an illustration of the choices a player makes to get to a game ending. Many devs use flowcharts to plot out their game before starting on the script, which helps the team calculate the project’s scope. Some VNs will offer an in-game flowchart to keep track of which routes the player has explored. Alternately, a flowchart may be offered on their website, in an artbook/fanbook, or created by a game’s fans.