The story branches based on the choices you make and it affects which escape rooms you will encounter. In the flowchart, you can warp to any previous story point and see the outcome of different paths. There are multiple endings and some paths lead to game overs. If you encounter a lock that is preventing further progress, then you are missing some information that is obtained from another path.
Each escape room has a safe that contains a key that will allow you to escape. To open it, you will need to solve puzzles to obtain the safe password. There is an additional password that can be used on the safe to obtain a gold file (hard difficulty) or silver file (easy difficulty). The gold file contains everything in silver file. The gold/silver file is not required to complete the game, but it provides additional background and lore.