Once you've researched the part where you get fleet supply cruisers (i.e. you have researched deep sea operations), you've essentially reached the end of the arc. You can already get HSD Lab and Marine Base attacks, for example, it's just RNG from now on.
The underwater arc does not have any finale or real reward such as some other arcs. The main benefit of the arc is easy money from undersea city/tasoth factory and all the juggernaut suits you can farm from the gillman heroes.