The story takes place shortly after the end of Crysis 2, in which Alcatraz retells the events in Crysis 2 from his own perspective to a CSIRA Blackbody Council. The story concludes with the Council wondering about Alcatraz's current condition from integrating with the Nanosuit 2.0 and about the Ceph's campaign on Earth, pondering whether it was nothing more than an mere irrelevant investment or if their true motive was to retrieve their technology stolen by Jacob Hargreave.
- Crysis: Legion is the only context in which Leavenworth is mentioned by name.
- The organization conducting the "BlackBody Council" investigative hearings at the end is identified only as "CSIRA". This is a reference to Watts's earlier (unrelated to the Crysis universe) novel series, the Rifters Trilogy. In those books, the acronym stands for "Complex Systems Instability-Response Agency."