[Update: This press release from Sega Sammy confirms the acquisition. It also notes Sega's intent to leverage Atlus IP in several ways. Aside from continuing making console games, there is mention applying gained IP to Sega's burgeoning PC and mobile fields. It even notes using the gained IP in Pachinko machines. The "Sammy" in Sega Sammy Holdings is notable for its production of Pachinko machines.]
Atlus will finally be under new ownership, according to reports from Nikkei (Nihon Keizai Shimbun), translated by Nintendo Everything. We previously reported that Sega expressed interest, among other suitors, in buying Atlus.
According to Nintendo Everything, Sega Sammy is in fact buying out Index Holdings entirely, which would simultaneously put the Persona developer in its stable. The 14 billion yen transaction is expected to be finalized in November.
Sega, remember what you did with Valkyria Chronicles 3? Don't do that anymore.