Gameplay diverges from the previous game: battles take place in real time and the area of action is less restrictive.

There are also no random battles; enemies will be found wandering in plain view, hence allowing the player to avoid confrontations and plan strategies.

[2] Equipment can be obtained through various methods, including finding, purchasing and 'creating' items such as body armor, weapons, ammunition and tools.

While Aya can only carry limited amounts of equipment with her, inexhaustible ammunition boxes exist in most areas and can be revisited as often as required for a top-up.

Armor, which not only reduces damage but also affects the amount Aya can carry, has the option of adding extra item slots up to a limit of ten.

In September 2000, nearly three years after the events of the first game, Aya Brea, now an FBI operative working in the clandestine Mitochondrial Investigation and Suppression Team (MIST) department; is dispatched to the Akropolis Tower shopping mall in Los Angeles as back up the LAPD SWAT team in response to reports of Neo-Mitochondrial Creatures (NMC) sightings.

As Aya and her partner Rupert Broderick investigate the tower they discover a new form of NMC with the power to pass as human which was able to slaughter the first SWAT team responders.

Following the raid Aya is sent by MIST director Eric "Hal" Baldwin to investigate the desert town of Dryfield, Nevada, over reports of unusual animals.

While initially displeased with the assignment, Aya learns from MIST's technical expert Pierce Carradine that an implant recovered from one of the new NMCs has desert sand unique to that area of Nevada near Dryfield.

Originally intended to be a showcase of ANMCs with multiple different habitats and viewing platforms, Neo-Ark was ground zero for the outbreak of creatures and has also been overrun by various kinds of NMCs.

9 attempts to use Eve to hatch the monstrous ANMC when Kyle betrays him, revealing he was a double agent sent to infiltrate the Shelter's conspiracy, and allows No.

At the same time, to contain the threat of the NMCs, the US President orders the use of a Satellite Weapon to destroy Dryfield and the Shelter, prematurely hatching the ANMC.

In the aftermath Aya adopts Eve as her younger sister, Rupert takes over as leader of MIST after purging the corrupt elements of the organization, and Pierce begins work on a plan to reveal the existence of Neo-Mitochondria to the public.

During development, it was decided to turn the game into an official sequel to Parasite Eve, making Aya the main protagonist and removing Kyle as a playable character.

[4] Using feedback from the original game, the team decreased and smoothed the transition between exploration and battle, and adjusted the controls to be more user-friendly.

[3] The character of Aya had been created for Parasite Eve by the producer Hironobu Sakaguchi, and designed by artist Tetsuya Nomura.

[6] After the game was done, the team was merged with those behind Brave Fencer Musashi, Mana and Chrono Cross to make Final Fantasy XI.

[7] The score for Parasite Eve II was composed by Naoshi Mizuta, serving as his first work at Square after leaving Capcom in 1998.

[14] In late 2000, the game was re-released as part of the Square Millennium Collection along with a figure of Aya and a portrait of her character model, Yumiko Shaku.

[16] In early September 2010, posts made on Twitter in relation to the spin-off title The 3rd Birthday suggested that Parasite Eve 1 and 2 would be added to the PlayStation Network's game download service.

[19] Greg Orlando reviewed the PlayStation version of the game for Next Generation, rating it four stars out of five, and stated that "Square seems to have taken to heart most of the criticism from the original.