Alright, It took me about an hour to figure all this out and sketch it all down, I'm sure I'll be updating it more as I learn more, and figure out more about how it works. Here's what I've got so far, if anyone is lost with starting their archival missions, I sure hope this helps!
Midian Park East - Machine Archivist
Moriah Projects East - Zion Archivist
Appolyon Northwest - Merovingian Archivist
You can start off by picking up each piece (mission) of the chapter you'd like at your organizations archivist, I'll explain it by using the first chapter.
Then go to a district of your choice, and start up the first mission in the chapter(1.1.1). Do this mission 3 times, and you will recieve the Completion Token 1.1. Once you have completed the first missions, and recieved the completion token, move on to the next mission in the chapter(1.2.1). Do this mission until you get your completion token, and then do the next and final mission in the chapter(1.3.1). Until you recieve the completion token for this mission as well. Once you've completed all the missions for each chapter, head back to your archivist to pick up the next chapter. Fire up the mission until you get the token, and so on, and so forth.
Once you've completed all 4 chapters for your organization, head to one of the locations below:
You will need the following completion tokens to recieve your organizations article of clothing:
Completion tokens 1.1, 1.2, 1.3, 2.1, 2.2, 2.3, 3.1, 3.2, 3.3, 4.1, 4.2, 4.3, and 4.4
Ikebukuro Northest - Machine Trader
Kaede Central - Zion Trader
Sai Kung Southwest - Merovingian Trader
(There's also a trader for each organization in Richland, Westview, and Downtown, I believe)
The items you will recieve are as follows:
Machine - 10% IS Regen Shades. (look alot like the glasses agents wear, they differ from void shades but they ALSO have the 'earpiece' on them.)
Zion - 10% IS Regen Barret
Merovingian - Melee, Thrown, Viral, and Ballistic damage resistance (11points to each) coat
After you've traded your completion tokens for your items, you can move on to the next organization if you chose, but keep in mind that you also have to run the missions again for your org. (so if you're machine and you got your shades, you're gonna have to run all of the missions from all of the chapters again to get another one of the orgs items)
There's also 4 other items you can get, I'm not sure exactly what they do, yet, I hope to get at least the first one tonight. But here's what you're gonna need to recieve these items:
Completion Tokens for Chapter 1 for all three organizations
(Zion, Merv, and Mach Completion Tokens 1.1, 1.2, and 1.3)
-Noninfectious Flame Virus-
Completion Tokens for Chapter 2 for all three organizations
(Zion, Merv, and Mach Completion Tokens 2.1. 2.2, and 2.3)
-Noninfections Fly Virus-
Completion Tokens for Chapter 3 for all three organizations
(Zion, Merv, and Mach Completion Tokens 3.1, 3.2, and 3.3)
-Fly Storm-
Completion Tokens for Chapter 4 for all three organizations
(Zion, Merv, and Mach Completion Tokens 4.1, 4.2, and 4.3)
-Blue Headlamp-
I think that's just about it, if I left anything out, feel free to let me know. I sure hope this helps you guys!