Also I believe the previous mission door from the previous exit out of the Cryptic Map will still be available which may lead to the player getting stuck in a loop. Not sure if this is still the case post publish though.
I suspect this is one of those things where it didn't occur to whomever designed the Foundry that we'd want to go from a Cryptic map to a custom map and then back to a Cryptic map. Can't think of everything, right? lol.
RE said last night he was a little confused by my post, so here's the detailed version: When I made my mission that has this issue (which is called "Over There" btw), it was right after the Season 4 downtime. Essentially it has you talk to a contact in Starfleet Academy, then go to the door at the end of the hall to transition into a custom map, then you go back out and talk to that academy contact again, then enter a door on ESD which takes you to the rest of the mission. And at the end, you have to go back to talk to that academy contact a third time.
This was also before the big storyboard change. Originally, when you were done with that first custom map, you had to press the "Beam Out" button by the minimap to exit as no map transition would pop up (there was none on the storyboard either). I had to add some text to the dialogue telling people they had to do this. It would send them back outside the entry door at the Academy, and there would still be an option to re-enter the custom map.
After that big storyboard change (was that Season 6? I forget), suddenly there was a map transition from that custom map back to the academy. But it isn't in the storyboard so I can't change it.
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I would love for this to work, as not only does it allow us to incorporate different locations to travel to during the mission, it also allows a "break" in the story, like we've seen during the episodes. Right now, the player is pretty much stuck doing the entire mission as is, regardless of length.