Afternoon of Darkness features extras over the original title such as a 16:9 format, to take advantage of the PSP's widescreen display. There is also a mode that focuses on Etna as the main character. In Etna Mode, Etna kills Laharl by accident while trying to wake him in the beginning of the game and thus becomes the main character. There are some extra boss battles such as Overlord Zetta from Makai Kingdom and Rozalin and Adell from Disgaea 2. There is, for the first time, a multiplayer mode available through Ad-hoc connections. This features multiple modes such as a "Defeat the Leader," "Capture the Flag," and the original "Battle." In the Multiplayer mode, each player also has access to "Geocubes" which give different effects to the battlefield. Other new additions include a music shop, which allows the player to listen to the game's various songs and even change the Item World theme, and a record keeper, which keeps track of various bits of information such as ally kills and obtained items.
In addition, Afternoon of Darkness includes a complete dual language option and the option to turn off battle animations, both of which have been included in recent Nippon Ichi games such as Disgaea 2 and Soul Nomad. Most of the Japanese cut scenes that were originally voiceless now include voices, though some of cut scenes are still voiceless. However, when set to English, the scenes that were originally voiceless in the PS2 release are still voiceless. To reflect Etna's recent voice actor change, her lines have been re-recorded to match Michelle Ruff's portrayal of Etna in Disgaea 2 and the anime. One notable omission is the theme song "The Invasion from Within" by Tsunami Bomb. As ATLUS was the publisher of the original PS2 version (and as such arranged for the licensing of the song) and NIS America (Nippon Ichi's own American branch) published the PSP port themselves, they did not retain the rights to use the song and did not renegotiate for them. Also missing is the song "One With the Stars" which, like "The Invasion from Within", was added in the original PS2 release by ATLUS.