I have gotten the option to side with either captain Ironsides or the scavengers midway through the quest. Up until meeting the Scavengers, Ironsides seems like a nice guy. Is there any good reason to betray him and side with the Scavengers?
The short answer is no, there is no going reason to betray him. Wipe out those filthy scavengers! Ironsides will give you a nice quest reward and you get nothing worthwhile siding with the scavengers.
Warning, quest related spoilers ahead. Don't read if you want to side with the scavengers anyway.
If you side with the scavengers they will betray you in the end. Once they get what they want they turn hostile and you are now left in a position where you have put in all that hard work for nothing. This is the main reason not to side with the scavengers, but there is also another big one. You will get a really good quest reward from Ironsides after completing the quest. You will get a large gun that shoots cannonballs. Ammo isn't too common, but it's not a gun you will be using during your day to day tasks.
It's a no-brainer. Screw the scavengers over and side with captain Ironsides.
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