More unresolved plots involve the Black Organization:
What is the real name of the Black Organization ?
The true significance of the Black Organization. Is the BO international ?
Besides Vermouth, Kir, Rye, Sherry and some known Japanese operatives, where do the rest of the BO come from ?
The true age of all the BO members (including The Boss).
How many code-named operatives does The Boss have ? Is there any unknown executive member other than Gin, Vermouth and Pisco ? How highly ranked are Sherry and Bourbon ? Is Vermouth The Boss' only favorite ?
Where exactly is the Black Org. Headquarter/main hide-out/The Boss's living place ? Is it located somewhere in Tottori after all, or another location ?
The exact time of when the BO was established. And who are the original members ?
Has there been any boss-changes during all these years ? Or is Anokata the only Boss from the beginning ?
Has The Boss ever changed his living place/hide-out ?
For exactly how long has he/she used "Nanatsu no ko" to encode his/her phone number ? (I.e for how long has he/she used the number #969#6261, which may have Tottori's area code ?)
Why does the boss use Nanatsu no ko? Is it a reference to something or some kind of inside joke?
Where exactly do the other BO members (except Vermouth) spend their time when they're not having any mission ? Do they "return to The Boss's side" or do they have their own hide-outs ? What do they eat and where do they sleep everyday ? Why are they usually shown hanging out at shipping yards for various reasons ?
Besides Vermouth, are the other operatives even allowed to meet The Boss face to face ? Do they even know his/her identity ?
Do The Boss and the rest of the Org. know about Vermouth's non-aging condition; or they just simply think that Sharon & Chris are 2 different operatives ?
Do they have missions anywhere other than Tokyo ? (Notice the robbery syndicate in Tottori).
The Boss's, and all of the operatives' past or childhood in general, and how they ended up in the BO.
Aside from the APTX-project and Itakura's program, does the BO have any other project/interest ?
What, after all, makes Gin so suspiciously loyal ?
Does The Boss trigger Haibara's "BO sense" ?
What exactly is the purpose behind this whole "crow symbolism" thing ? Does The Boss really like crows that much ?