Phantasy Star II takes place 1,000 years after the events of its predecessor and follows the journey of a government agent named Rolf and his friends, who are on a mission to discover why the protector of the planet Mota, Mother Brain, has started malfunctioning.

Its battle system is turn-based as well as menu-based, allowing the player to choose commands for their party of up to four characters.

Once a dry desert planet infested with ant lions, Mota has been transformed into a blue and green tropical paradise.

Being part biomonster, she is an outcast from society, causing her to loathe mankind and, because of this, sabotage both Mota's climate control system and the biosystems laboratory.

Anguished, Rolf and the remaining party defeat Neifirst, causing the biosystems laboratory to self-destruct and bringing an end to Mota's Biomonster hazard.

However, this sets another incident in motion: the explosion of the lab damages the Climatrol equipment and causes the central lake, the residential reservoir of Mota, to overflow with water.

After unlocking the last one, they are captured by Mother Brain's security robots, charged with causing the environmental disaster, and sentenced to death upon the Gaira satellite.

Now the system's most wanted criminals, blamed for Palm's destruction and the deaths of its people, the group boards Mota's last remaining spacecraft – legacy of a space program now falling into ruins – to the mysterious and dangerous Dezo.

Located at a far corner of the planet is the Esper Mansion: upon reaching it, Rolf awakens the legendary Lutz from a long sleep.

In order to save the System, the heroes seek to recover the powerful Nei arsenal, found in four hidden dungeons, capable of defeating the enemies on the spaceship Noah, where Mother Brain resides.

They reveal they created Mother Brain to satisfy their greedy lifestyle at the expense of Algo's resources, and a fight between the heroes and the earthmen ensues.

The game is also included as part of Sega Genesis Classics for Xbox One, PlayStation 4, Nintendo Switch, Microsoft Windows, macOS, and Linux.

On September 28, 1994, both parties reached a settlement involving a cross-licensing agreement to publish up to five games each year across their systems until 2001.

Phantasy Star II was one of the first five games approved from the deal by Sega in order to be converted for the Atari Jaguar, but it was never released.

"[12] Wizardry designer Roe R. Adams wrote in Computer Gaming World that Phantasy Star II was a system seller for the Genesis,[22] stating that its "16-bit graphics are gorgeous, but the real fun lies in the science fiction story plot."

[28] It was the first RPG for the Mega Drive, and was released in the U.S. two months before the original Final Fantasy for the NES, another key game in the genre's popularization in North America.

[31] The game's science fiction story was also unique, reversing the common alien invasion scenario by instead presenting Earthlings as the invading antagonists rather than the defending protagonists.

[34] In 2003, IGN ranked it as the 92nd top game, choosing Phantasy Star II for how it "surprised everyone with the death of a major player 1/3 the way" years before Final Fantasy VII, in addition to "a balanced experience point system, tough-as-nails bosses, and one of the biggest and most difficult RPG quests that we've ever seen.

Much like Phantasy Star Generation 1, the remake mirrors the events of the original game while adding character development and fleshing out the story in more detail.

The compilation's future is uncertain, however, since Sega reclaimed the publishing rights for North America and Europe.