Accidental sequence break?

After reaching the marsh and failing to beat Legion, I decided to visit old biomes to collect some stuff I missed. Teleporting to the bridge allowed me to lower the bridge into the city, which ended up with me dying to the Architecht and being very confused when Stack and Bouchard were suddenly dead on my return.

Finally ended up beating Legion and saw the cutscene with bouchard getting blasted, and now I see Im supposed to "explore the marsh" as my quest to somehow facilitate the bridge component being fixed, but when I get into the biome the only quest markers are for killing the architect. Dont want to miss out on any content by skipping ahead but Im a little confused what Im supposed to be doing