A research company rising in power and influence, they are responsible for breakthroughs in AC development, and also serve as sponsors for the Ravens' Nest Arena. The company eventually becomes the player's sponsor in the Arena. Within PROGTECH is the head of R&D, Elan Cubis, a brilliant scientist, and contacts the player via mail in later portions of the game.
The main character is a Raven seeking revenge against the number one ranked Raven Hustler One and his AC Nine-Ball. Prior to the game, the Raven's family along with many other civilians were killed in a violent skirmish between Chrome and Murakumo Millenium in Isaac City, with Nine-Ball at the center of the conflict. After encountering Nine-Ball again during the Raven's first mission, his contact Lana Nielsen tells him about the Arena, and that if he wants to defeat Nine-Ball, he must climb to the top of the Arena, but challenging him may result in death.
After completing more missions, the Raven is contacted by PROGTECH offering to be his sponsor in the sub arena, and eventually the main Arena. During points in the story, the Raven's Arena licensed is revoked temporarily in order to aid PROGTECH in a critical mission. However, these are mission requests being sent directly to the Raven, rather than through the Nest's channels to the Raven's operator. The Raven receives his first warning from Lana after completing one of these direct mission requests, and after doing it a second time, Lana Nielsen ceases to be his operator, leaving him in the dark without new contracts to accept. The Raven has no choice but to continue fighting in the Arena until he can face Hustler One.
PROGTECH continues to face attacks from unknown forces, this time at their head of R&D Elan Cubis. The Raven comes to his aid, and Elan agrees to assist the Raven in anyway he can for information regarding Hustler One and Nine-Ball. Cubis discovers that all important files pertaining to Hustler One and Nine-Ball have been deleted, and sources claim that no one has ever seen Hustler One in person. After reaching 2nd place in the main arena, Elan Cubis goes into hiding for fear of Nine-Ball coming to assassinate him, and Lana Nielsen returns to give one final mission to the Raven. In an abandoned factory in Isaac City, the Raven faces against Nine-Ball, and then two more Nine-Balls at once, all with Lana Nielsen's voice, albeit distorted. Lana Nielsen is revealed to be Hustler One, and that Nine-Ball is controlled by an AI, similar to the first Nine-Ball and "R" from the original Armored Core. After destroying the three copies, the Raven descends further into the complex and discovers the ultimate form of Nine-Ball. Nine-Ball Seraph, a more powerful and deadlier version of the red and black AC. The Raven defeats Nine-Ball Seraph, and with the destruction of Hustler-One, the Ravens' Nest functions ceased to operate.
Gameplay is identical to Armored Core and Armored Core Project Phantasma. With new parts introduced, previous parts were adjusted to better balance the game. Like in Project Phantasma, the player can transfer data from either the original Armored Core or Project Phantasma. Secret parts in the original Armored Core could not be obtained in Project Phantasma, but in Master of Arena, they are available in the shop from the beginning.
The Arena concept from Project Phantasma has been expanded, and is now integral to progressing through the main game. The player cannot enter the Arena proper until the player's AC is backed by a sponsor. At points in the game to progress the story, the ability to compete in the Arena will be revoked in order to focus on critical missions for the Raven.
Armored Core Master of Arena came with two discs. The first disc contains the mission mode, sub arena, and main arena. On disc 2 was the Ex Arena and Ranker Mk. Ex Arena provided 8 additional Arenas for the players to compete in, and Ranker Mk could let the player create their own custom Arena mode, including AI for the ACs.
In Armored Core Master of Arena, 27 new parts are introduced, bringing the final total of the PS1 Armored Core parts to 187. All previous parts in the series can be accessed in the shop, and some items have had stat changes along with the new parts in order to keep the game balanced.