*The series alternates between different sets of pairs. Although it's supposed to be read as a whole, you can skip volumes with the pair(s) you don't like (which is not recommended at all because the events in the Warui Koto Shitai universe still progressing in every new volume).

Warui side - Mikado x Towa (Pair 1)
Featuring the school delinquent Towa Aikawa and the student council president Mikado Shirahane.

• Volumes involving this pairing are:
  v01: Warui Koto Shitai
  v02: Warui Ko Demo Ii?
  v04: Warui Yatsu Demo Ii
  v07: Warui Koibito Ja Dame?
  v11: Warui Ouji Demo Suki

Ja Nai Kedo side - Ryuichi x Shūji (Pair 2)
Featuring Shūji Yukimura, the formidable student council vice-president, and the problematic childhood friend, Ryuichi Shinonome (Towa's friend).

• Volumes involving this pairing are:
  v03: Kirai Ja Nai Kedo
  v05: Koi Ja Nai Kedo
  v08: Kare Ja Nai Kedo
  v10: Sunao Ja Nai Kedo
  v14: Himitsu Ja Nai Kedo

Mujihi na side - Kuon x Nanao (Pair 3)
Featuring Nanao Shirahane (Mikado's older brother), a male siren, and Kuon Aikawa (Towa's older brother), a fellow student attending the same university.

• Volumes involving this pairing are:
  v06: Mujihi na Otoko
  v09: Mujihi na Anata
  v12: Mujihi na Karada
  v17: Mujihi na Yoru ni

Shouwaru Ookami ga Koi o Shita Rashii - Shirō x Nao (Pair 4)
Featuring former student council president, Shirō Akagi (Mikado's rival in Warui Koibito and Warui Oujii) and disciplinary committee member, Nao Kousaka (Yukimura's rival in Sunao ja Nai Kedo). How will those two damaged people find their respective love?

• Volumes involving this pairing are:
  v13: Shouwaru Ookami ga Koi o Shita Rashii

Warui Koto Bakkashite Gomen Nasai - Mikado x Towa, Ryuichi x Shūji, Shirō x Nao, Kuon x Nanao (All pairs)
What will happen when a few teens enter into an unexpected drunken state?

Kira Senpai to Kokonoe-kun - Makoto x Tōru (Pair 5)
Featuring Makoto Kira, the head of the journalism club, and Toru Kokonoe, his junior and the only member of the club, a foul-mouthed, cocky little brat who suddenly finds himself attracted to Kira.

• Volumes involving this pairing are:
  v16: Kira Senpai to Kokonoe-kun

Reading Order
taken from the official website:

(Volume number - Title [Pair number - Appearance number])
+ Pair 1: Mikado x Towa
+ Pair 2: Ryuichi x Shūji
+ Pair 3: Kuon x Nanao
+ Pair 4: Shirō x Nao
+ Pair 5: Makoto x Tōru

v01: Warui Koto Shitai [1-1]
v02: Warui ko Demo Ii? [1-2]
v03: Kirai ja nai Kedo [2-1]
v04: Warui Yatsu Demo Ii [1-3]
v05: Koi Ja nai Kedo [2-2]
v06: Mujihi na Otoko [3-1]
v07: Warui Koibito ja Dame? [1-4]
v08: Kare ja nai kedo [2-3]
v09: Mujihi na Anata [3-2]
v10: Sunao ja nai Kedo [2-4]
v11: Warui Ouji Demo Suki [1-5]
v12: Mujihi na Karada [3-3]
v13: Shouwaru Ookami ga Koi o Shita Rashii [4-1]
v14: Himitsu ja nai Kedo [2-5]
v15: Warui Koto Bakkashite Gomen Nasai (Special)
v16: Kira Senpai to Kokonoe-kun [5-1]
v17: Mujihi na Yoru ni [3-4]

Notes:
- For a detailed guide of Warui Koto Shitai series, special chapters and releases, check this topic.
- 'Warui Koto Bakkashite Gomen Nasai' is officially considered the 15th volume in the series. And on June 19, 2020, it got a Digital re-print.