Summary X is piloting an airship above a Japanese city after receiving a message from Zero telling him that he has found Sigma's main hideout. Zero's message says that he will be going in first and that it's his job from here onward, ending with Zero thanking X for his hard work. X, frustrated by Zero's selfish decision and for not telling him the whereabouts of Sigma's hideout, speeds up but is interrupted when his airship sensors begin to act strange. X looks outside, and watches as a massive tower emerges from the ground destroying part of the city below. The tower begins to charge, and unleashes a massive wave of energy, reducing its surroundings into a smoking crater with surrounding buildings toppled over. X watches in horror, but notices his airship sensors acting up again and notices the tower recharging several times with an energy reading much larger than earlier. X flies the airship upward, parallel to the tower while dodging turret fire. X fights off the tower defenses with on-board missiles, but one of the thrusters is struck by turret fire. X purges the damaged thruster, and rams his way into the tower.

Inside the tower, an alert is issued informing the Mechaniloid army to investigate Block 927 where X crash landed. When the Mechaniloids arrive, they find X's abandoned airship as X sneaks past them above. X attempts to make an escape, but trips a laser trap which triggers a laser blast to hit X, causing him to fall off the ledge. The Mechaniloids are alerted of X's presence, but are quickly dealt with. X rushes upwards the tower fighting off turrets and more Mechaniloids, but is eventually cut off by overwhelming fire. X notices a high-pressure energy pipe, and shoots a hole in it causing the liquid inside to spray out. Some of the liquid hits X, causing minor burns as a Mechaniloid says even X can't survive it for long. Ignoring the warning, X jumps into the energy pipe as the Mechaniloid laughs at X's stupidity, saying that the Rockman's going to be deep-fried with such a stunt. Enduring the immense heat, X rides the rising current of the liquid energy as he blasts a hole near the top, and is shot out of it landing right in front of the control center. X comments that it was a reckless plan, but it saved him a lot of time as a result.

X enters the control room, noticing how quiet it is but hears noise coming from all directions. X is then sliced by a sharp object several times, and recognizes this stealthy fighting style. Boomer Kuwanger appears, asking if X remembers their time as colleagues. Kuwanger continues by saying the tower's first experiment was a success, and that he wanted something more exciting like this unlike his boring days as a Hunter. X asks what's so exciting about all this as he fires a shot at Kuwanger, who accelerates at a great speed and dodges X's attacks. Kuwanger continues picking up speed, eventually disappearing from X's sight as he reappears beside X and unleashes a flurry of punches at X. X manages to dodge one of them and dashes away, but Kuweanger immediately catches up as X wonders if Kuwanger has exceeded the limits of a Repliroid. Kuwanger stops and throws his Boomerang Cutter at X, which X remembers as being capable of reducing Irregulars to sliced scrap back during their Hunter days. X knows Kuwanger is aiming for his neck, and blocks the cutter with his buster, leaving a massive cut on it. Kuwanger continues striking X at full-speed as X fires shots repeatedly at Kuwanger only to miss, but notices Kuwanger reappearing briefly when one of his buster shots hit one of the electronics on the ceiling. Kuwanger taunts X, saying that he better hurry though they'll be safe inside when the next blast goes off. Kuwanger tells X that the lights on the wall are the charge indicator, and to think of it as a countdown. Kuwanger continues to kick X down, boasting that he has been reborn. X notices what Kuwanger said and realizing what he meant, X fires a shot that hits through one of Kuwanger's legs, and straight to a core on the ceiling. As the core is destroyed, the walls surrounding the room break apart, revealing a massive computer brain which X realizes is Kuwanger's real brain, and that the tower is Kuwanger's true form and that's how he was able to push his old body beyond possible limits. X attempts to shoot at the computer brain, but even his charged shots are ineffective against it. Kuwanger says that his computer brain is protected by a special field that cannot be penetrated even with a charged shot. X realizes he needs a much stronger power source, and notices charging is complete. Kuwanger says that the blast is enough to wipe out Japan, as X notices several high power cables connected to the computer. X takes the risk and rushes to it, plugging the power cables into his buster overcharging it. Kuwanger says that X is charged with enough energy to reduce Japan to ashes and whether he is serious, but X says he's aware and forces out an overcharged shot that completely destroys the top of the power along with Kuwanger. The resulting shot tears through the power wall while everyone outside watches it.

The nearby army makes a run for it as the remains of the tower fall, destroying several tanks in the process. An army scout checks his scope, noticing someone on top of the tower. The scout identifies X, calling him "Rockman". As X makes his way down, the crowd cheers X by calling him "Rockman", but the celebrations ceases as Sigma's floating island fortress descends downward. Sigma calls X by the title of "Rockman X", and invites X directly to take him on. X watches up at the island fortress as an army commander is about to give orders to fire in the name of mankind. However, he notices X getting aboard one of their airships as he is rallied by everyone else. The commander notices X's broken buster, saying X is only going to get himself killed. Without even flinching, X gets on the airship and heads towards Sigma's floating island fortress.

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Commentary The Boomer Kuwanger arc marks the last of the boss story arcs, leading directly to the final confrontation against Sigma. Being an upward climb, introducing this stage through parts of the game felt appropriate though thankfully shortened by X's shortcut through the energy pipe that took him straight to the top. The inclusion of a Mechaniloid army being directly referred to does give off a more "last stage" vibe, and given the tower's ability to wipe out countries it makes sense that a structure like this would be heavily guarded. Interestingly, one of the Mechaniloids referred to X as the "Rockman"; does that mean even the grunts have been briefed on it big Sigma, or did this one just hear it from somewhere and is one of the exceptions?

Being a logic and data-obsessed character, Boomer Kuwanger moving his main brain into a much larger and powerful enclosure (in this case, the entire tower itself) felt in-character for him, albeit taken to quite a logical extreme. Thinking back to the previous chapter, does that mean Repliroids are capable of being freely transferred in some form (much like with Marty to a lesser extent), or are these just narrative exceptions?

I'm not sure if this was intentional, but the aircraft X piloted at the beginning, shooting a core during a boss fight, then followed by destroying a giant brain at the end just felt like a shout-out to Gradius; specifically with X's aircraft having Vic Viper's characteristic double-pronged fuselage, boss fights involving shooting an enemy core, and the last sequence involving the destruction of a (sometimes shielded) brain. Another one that's probably just narrative coincidence is the gamble of using all of Japan's energy for a beam-based attack reminded me of Operation Yashima from the Evangelion series.

Now with all 8 boss story arcs concluded, the last two chapters would be the final battle. In X's damaged state, it'll be interesting to see how this will play out when compared to the games.