I thought Valkrye supposed to be Siege cause you do need that for nuke.About the Final Showdown quest. It is triggered at some point in the game after beating a guardian. We are asked if we want to keep the main mission (in this case nuke) or if we want to fight head on.
I haven't tested yet to see if this mission appears in my Alf run, but I suspect this mission is a workaround in case Alexa isn't set to the correct mode. (Alf/transport Valkyrie/production).
Or maybe it's even a 'happy ending' workaround since Seidr and the game itself is also bugged.