Ninja base question

[Ruberto]

Hello
I have a question about ninja bases
In my play-through, I have several smaller ninja hideouts (approached in transport, square outer wall, central tower) and one stronghold (approached on foot, line of bunkers with airfield behind it).
I am thinking about attacking the stronghold. I see it will be very long, painful and costly mission.
Question: after I destroy the stronghold, will ninjas disband and smaller bases disappear?
Or will one of the smaller bases become hq and morph into the stronghold soon after I destroy the current one (so I should destroy the small bases first?)?
Also does destroying all ninja bases ends their threat or i will need to unlock some special mission to end them?

[legionof1]

Killing the bigger base wont remove the little ones, but it will stop more outpost from being spawned, assuming the base has not already made the max for its level.
The little ones will stay as they are. I would generally advise you do one or 2 small ones first just to loot some emp greandes to ease your way with the big base.
And no ninjas will still be around even if you wipe out all the established bases and outposts. Just a less dominating presence on the map, more in line with the other factions like the guild. 

[qwertzy]

While everything relevant has been said already, as a side note, the stronghold will be two missions at once, so don't be too wastefull on the first map (though the first part seemed harder to me due to less cover in the beginning).