The story starts after 1st season and before Darker than Black Gaiden. Hei (BK201) and Yin return to Tokyo to investigate how a Black Dandelion is granting Contractor-like powers to people who come in contact with it.
I don’t believe the description in myanimelist which says that that this manga replaced all the events of the 2nd season completely. Whoever wrote that might be a disappointed fan who watched the 2nd season and/or have not seen DtB Gaiden.
This manga takes place after the 1st season and before the OVA. But it foreshadows the events that were about to happen in the OVA and the 2nd season. Though Hei is still the main character, much of the focus is on a girl named Azusa Tsukimori, a high school student and volleyball player, who desires to become a Contractor after she found out that her volleyball coach posted naked pictures of her in a porn website. Until one day, she met Harvest, a Contractor who can give Contractor-like powers.
I like how the characters were developed in this story most especially Hei and Yin and the other Contractors. There’s lot of action here as always and sometimes when I read this manga, I played the OST of Darker than Black: Ryuusei no Gemini since it has a more epic tone than the 1st season’s OST. The art style is done by the same character designer of the anime series but somehow, his style reminds me of Bleach.
This manga is just a bonus for those who love the Darker than Black series. But you may get to understand the events of the OVA and the 2nd season better if you read this.