Basically, how do you have branching dialog that triggers objectives based on what you said? Like Negorak's (I think it's his) mission on the frozen moon where at the end, you have to choose to go left, right or straight on, and it's a different mission ending objective depending on what you do.
A Romulan Strike Team, Missing Farmers and an ancient base on a Klingon Border world. But what connects them? Find out in my First Foundary mission: 'The Jeroan Farmer Escapade'
You need to have a map object dialog be trigger which contains your options. Option 1 through 9 for instance.
Once the player has selected (and perhaps confirmed) their option then you trigger things using Dialog Prompt Reached trigger for that option. From NPC groups to other interactables and walls or other blockages to stop the player from reaching other option-based areas.
You can only really use this for optional tasks as of yet, you can't initiate an alternate mission direction this way. That would require a major upgrade to the foundry system which you likely shouldn't hold your breath for. Even if it did become available you would likely have to make a full, alternate version of the mission from that point on each time you did it.
Like the other replies said, basically you have to put one objective at the end of your map and have everything in between done with triggers.
I've done something like that in my mission "Over There," where at the climax of the story, the player can choose to activate a console or not to activate it. The objective is simply a reach marker with text that says "Make your choice and escape."
If you activate the console the villain yells at you and you have to fight your way out. If you don't activate it you're clear to the escape point.
I carry this through to the next map by asking the player what choice they made in a map dialogue at the beginning. Depending on the choice, it either spawns enemies or allies. In the final dialogue on a social map I again ask the player what they chose. Depending on the choice, they either get chewed out or commended by Starfleet.
So you can make the illusion of choice for the player and have multiple endings, but your objectives and the maps have to be linear.
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I would really like to see the ability to make branching objectives. That would really come in handy. I have a neat idea for a mission where a star system is about to go supernova, and there are several colonies in that system, but you only have time to evacuate one and you have to make a choice--the head of a civilization's government, an endangered sentient race about to go extinct, etc. There's so much more we can do with that. But that's an interesting workaround. It's like you choose later according to what you did earlier, and otherwise you don't notice.