Batman Beyond was published as an ongoing series that lasted for 8 issues, set a short while after the events of volume 3. It featured two major storylines, the first of which featured the Justice League Beyond and a person who would became the Matter Master of the future. The second storyline featured the return of Blight, Terry's original nemesis. Two issues also provided an in-depth exploration of characters Max Gibson and Inque, whose origins were revealed. Several plot threads were not resolved and left for 2012 relaunch.
This series also sees Terry McGinnis joining the Justice League, Dana breaking off her relationship with Terry and the introduction of Doug Tan, the soon to be Joker King. This series further strengthens the Beyondverse's connection to the mainstream DC Universe, although it is mentioned in the letter column that all events that happened in the animated series, the animated movie Batman Beyond: Return of the Joker and the first two volumes (1 and 2) still took place and have yet to be retconned. This means while all DC animated universe events should be canon to the Beyondverse, it is not always clear what mainstream DC universe events took place.
- The Heart of the Matter
- Industrial Revolution
- Issues #4 and #8 are the first of the Batman Beyond "Legends of the Dark Knight" issues, which are single-issue stories focusing on certain characters of the Batman Beyond series.
- Issue #4 is also the first issue to mention Undercloud, an underground organisation of computer hackers, which becomes an important subplot in Batman Beyond (Volume 5).
- Issue #8 sees the return of Dr. Thawne who was seen in the previous volume, also in the last pages of the final issue.
- In this series 'Wayne-Powers' becomes 'Wayne Incorporated'. This happens in the same issue that Batman Incorporated is first mentioned in the Beyondverse.
- Teen Titans and the Outsiders are also mentioned and brought into Beyondverse canon in this series.
- Superman/Batman Annual #4 served as a 'prequel' to the current series of Batman Beyond Comics, as stated in the letter column of Batman Beyond (Volume 4) #3.
- The Beyondverse Ace the Bat-Hound changes between having no collar to having a blue collar throughout the volume.
- Neo-Gotham is shown to represent class stratification through city levels; the lower the level, the lower the class of citizen. This is shown in Batman Beyond (Volume 4) Issue #7 were the lower levels are referred to as the 'dreg levels'.