Raise the Banners: Amnoon Arbitrator

https://wiki.guildwars2.com/wiki/Raise_the_Banners:_Amnoon_ArbitratorAfter I choose one of the items, how can I get the other two? If I go back and replay the story on the same character will that work or do I need another character and need to choose a side to play that was different from my first choice?

You'll need another character and choose the side of the banner you are missing the first time you play that mission with it.And it's not just the mission where you choose the side your siding with, but several other steps of corresponding banner collection as well that you need to do with that character.

So three characters in total, one supporting independence, one supporting joko, one supporting the sunpears to get all the banners.