(Spoilers ahead)
Hey, to answer your question, the response we give the co-workers on what action to take will affect the outcome of the RPC scenario, such as reducing or increasing your reputation points. Leaving your bunker while at the time, doesn't serve an in-game purpose, my plan is that the outside of the bunker is where you will receive physical items dropped off to you, which will help the gameplay. The main antagonist I plan to add in the story, Church of Maltus soldiers, have drones which scouts the El Salvador forest, and if they spot you while they are shining their area at a specific area outside which you are on, it will alert the maltus soldiers.
With Church of Maltus, the in-game universe states that they are trying to set up a new facility/training camp in Central America, such as EL Salvador. The Maltus members have no idea that RPC Authority members are stationed around the area, and they ain't expecting you, as they use the drones to find civillians/witnesses. RPC Authority personnel meanwhile, are attempting to spy on their plans, which means that no action against the Maltus members in that area can be taken yet, to avoid alerting the snakes in the grass. (This means Authority can't just send a MST team after them yet to protect you)
Anomalies the player will deal with indirectly will also affect the player directly, classic examples including cogintohazard/infohazards. However, there is way more to that. Take RPC-471 for an example, the first RPC being added to the game. In the second day the Rebecca girl, the one you talk to who's assigned with dealing with RPC-471, will be "missing" in Day 2. The player would have to decide to whether to convince the research team to find Rebecca (not enough clearence means less voice), or to obey them and keep researching on RPC-471 (Spoiler) RPC-471-C is suppose to have abducted Rebecca because shes one of the many who's interfering with their plans.
The player will also be stalked and attacked by RPC-471-C instances, both online and offline. This can come in the form of popups, being emailed by RPC-471-C instances, and RPC-471-C physically appearing in your bunker and attempt to kidnap you. My plan is that RPC-471-C will not instantly cause a game-over for-sure, but will knock you out to threaten you to give up interfering with them, or take you to the red-room and kill you depending on how you replied to their email messages.
In the case of RPC-471, the player is able to talk and negociate with the anomalies themselves, deciding to work out a hostage deal on their terms, or just say "fuck it" to them and do something else, whether its convincing the research team to track down Rebecca's location and save her, or leave her to die to focus more on stopping the RPC. How you reply/interact with 471-C online can also affect how they behave physically in your bunker. (471-C leaving you alone for an example if you choose to sacrifise Rebecca, etc) and many more.
That's an example with RPC-471-C itself, there are many more RPCs that will be included, where your choices will result in many different approach to the scenarios.
My plan is to add more with list of things to do. While email and computer interaction is a core mechanic to explore the story. Direct interaction with RPCs I agree with you, would for-sure make the story more intresting, such as more visual elements of how your actions/choices affect you and your surrondings. I plan to add more anomalies which the player will encounter physically and on-line where he will have to instruct personnels. I want to pick more RPCs on this wiki which can affect people without being confined in their physical locations. In the case of RPC-471-C, I felt that works for my goal because those instances are not 100% contained in one area.
I do like your idea of you being a lost agent being trapped, this would add more "meat" to the situation. I'm thinking to capture a simillar goal, prehaps the player can have the ability to "report" anomalous and/or hostile situations around them, and then using email messaging, the responding personnel will decide how they will handle your situation, based on what you say. It will add more intresting importance/interaction with just sending out emails.
Thanks for your feedback.
EDIT: I'm thinking if the player fucks up bad, for example on containing a world-ending RPC, the player will also witness the world end, as the apocalypse happens around him. In most cases if the player fucks up bad, he will be demoted which results in a game-over/bad ending. Also the player's choices will determine different ending/reviews on the player's actions.