Years have passed since the incident at the Silent Line, and with it the collaborative effort began by the Corporations in response to it is long gone. The battle between the Corporations has re-emerged and continues unabated. Now a new Corporation has entered the scene; this Corporation, Navis, while nowhere near the size of the other Corporations, does have a trump card; it has complete control over a brand new and very useful resource, and they don't intend to share. The other Corporations obviously won't sit back and let that stand, so they set up contracts with Ravens through Raven's Ark. Of course, Navis is employing the use of the Ravens as well, and a full-scale conflict seems apparent on the horizon. Once again, you are thrust into the lines of corporate warfare, but does something even more dangerous lie in wait?
- Raven’s Ark - The successor to Global Cortex in the region in which the game takes place. Like its previous incarnations, the Ark (as its known in shorthand), is a neutral "mediation" organization responsible for setting up contracts between Ravens and the Corporations. The Ark has only one primary stipulation: no Raven can directly accept a contract from a client without going through the Ark first.
- Mirage - The largest and most powerful of the Corporations. Despite their impressive strength, Mirage is still expanding into the region and is meeting with fierce opposition from Navis, a smaller corporation already heavily entrenched in the region. Mirage has its eye on Navis' unique assets and is not above starting a war to acquire them.
- Crest - The second largest Corporation behind Mirage. Crest is also working its way into the region but seems to be too concerned with self-defense and preservation than to stick its nose in the escalating conflict between Mirage and Navis... well, at least not too often, and only when there's an advantage to do so. If push comes to shove, however, Crest has an army of private AC pilots, led by the intimidating Raven known as Genobee, ready to step into the fray on its behalf.
- Kisaragi - One of the smaller Corporations. Kisaragi is a technical innovator always on the look out to acquire new resources and refurbish lost technologies to help their advancement. Kisaragi remains a primarily selfish and opportunistic player, offering aid with one hand and striking out with the other when the time is right. As it is, they have a small alliance with Navis for the time being. Should it come to war between Mirage and Navis though, Kisaragi's loyalty could go either way.
- Navis - A new Corporation formed very recently. Navis has a monopoly on a new resource and control over the region of the world where this resource can be found, and they aren't playing nice with it. Their all-out refusal to divulge any information on this resource, much less share it with the other Corporations, has led to rivalries and even conflicts with the other Corporations. Mirage is proving to be Navis’ chief rival.
- USE - A local weapons and MT manufacturer. USE tries not to involve itself in the current conflict and continues to remain neutral. USE focuses only on MT research and development.
- Organization for Administrating Enterprise (OAE) - A bureaucratic organization designed to police the corporations and keep them all in check. The organization is, for lack of better words, quite incompetent and is bullied into complying with the wishes of the larger corporations very often. Mirage constantly uses the OAE to its own advantage.
- Genobee - The most powerful Raven in the Arena. He works exclusively for Crest Industries, and is quite cold and enigmatic. He speaks in an almost robotic monotone voice. He pilots the all black AC Dual Face, which exhibits abilities beyond the capacity of other ACs. He commands the loyalty of other Crest-exclusive Ravens.
- Jack-O - A revolutionary Raven seeking to restructure the entire Ark administrative system. He is rarely seen in Nexus, but has a much larger role in its sequel Last Raven. He pilots the AC Foxeye.
- Evangel - A newly inducted Raven who becomes something of a friendly rival for the player over the course of the game. He is eventually expelled from the Ark for directly accepting contracts from the Corporations. The AC he pilots, Oracle, is featured on the game’s box art and heavily in its opening movie. He has a significantly larger role in the sequel to Nexus, Last Raven.
- Ammo - A rival to the player at the beginning of the game. He pilots the AC Birth Bomb which he later changes around and renames it End Bomb. He is killed when his AC is destroyed by another Raven on the battlefield.
- Agraya - Another AC pilot working exclusively for Crest. No official information on her exists as she is not registered with The Ark. She is extremely loyal to Genobee, evidenced both by the makeup of her AC Red Star, which has a similar all-black color scheme to Genobee's Dual Face, and by her regretful apology to Genobee after she is defeated by the Raven.
- Pin Fire - A Raven who appears in several missions working primarily for Navis. He is cruel and calculating and is killed by the player's Raven in a Mirage employed missions. His son is Rim Fire and is one of the few minor Ravens to survive the game and make a return appearance in Last Raven.
Armored Core: Nexus improves upon the Armored Core 3 game engine. The changes to the core system of the game are considerable, and so players are unable to import game data from the previous game, Silent Line: Armored Core or any other prior title.
The special feature known as "OP-INTENSIFY" has been taken out of the game, taking with it the useful yet debated performance enhancements such as "mobile cannon fire" while using Bi-pedal, Reverse-Joint, and Hover legs. The "blade beam" aspect of OP-INTENSIFY was kept intact and granted to all blades by default.
Removed features from gameplay are the clone weaponry as well as the weapon breaking previously available in Silent Line Armored Core. Many parts have been removed in transition as well. No longer are inside generator jamming rockets, inside ecm rockets, extension emergency energy coolers, extension stealth, back ammo magazines, or any howitzer weapon available to the player.
New weaponry includes railgun energy cannons, extension solid and energy rifle ammo magazines, linear rifle, new hanger weaponry, and side anti-missile field extensions.
Certain weaponry, mainly handguns, machineguns, and shotguns, now have limits to how many rounds they can fire off before they must reload a full ammo clip. This enhances balance somewhat in an attempt to curb up close CQ damaging racing tactics for players interested in Player VS Player gameplay.
Miscellaneous added features like Hanger Cores, the heat management system, booster heat, part tuning add new style to gameplay. Hanger Cores give players the option to take additional small weaponry like an extra hand gun or laser blade into combat, which can be deployed when the player drops their primary left or right arm weapon. Booster heat is a new feature where as when the AC boosts, causing the AC to heat up. This is now standardized in all types of boosting such as using the over boost feature.
The game is broken down into two discs, EVOLUTION and REVOLUTION. The EVOLUTION disc features all new content in which the story of Armored Core: Nexus is played out. Much like Armored Core 2: Another Age most of the game's arena battles are played out in story-based missions, however a "Free Arena" is unlockable upon completion of the Evolution game's storyline. The REVOLUTION disc takes a look back at previous Armored Core titles, primarily the PlayStation era titles; Armored Core, Project Phantasma and Master of Arena. Completing missions in REVOLUTION unlock extra parts for a player's AC which are based on parts that appeared in previous AC games, including custom parts featured on the AC of Project Phantasma's main antagonist, Stinger, now available to the player for the first time ever.
In the last mission, you get to face an old enemy from the original Armored Core series, albeit in different form: Nine-Ball. However, it was later revealed that 'Nine-Ball' was a prototype Pulverizer, shown in Last Raven. In the Japanese version of Nexus, the name read as '???'. Where Nine Ball came from was either from error, or because the translators thought it would be enticing to feature the old enemy. Despite the errors, this enemy does share similarities to Nine Ball, such as the use of weaponry like the grenade launcher, missiles, and an energy pulse gun, as well as the signature red armor color.