The Arsenal

The final encounter in Final Fantasy Legend II for the Game Boy takes place between your party of four characters, the goddess Isis who becomes your ally, and the security system at the central of the game's last area, the center of the Celestial World. The security system is comprised of two separate identical robotic weapons slightly resembling the classic Dungeons and Dragons beholder. Each of these is called an "Arsenal."
 

The Final Battle

 
For the last actual battle in which your party must engage, you will be facing off against one of these robots while Isis takes on the other by herself (she is, after all, a goddess).
 
The Arsenal has three main phases of attack before it will ultimately succumb to your maneuvers, with each phase being accompanied by a different musical backdrop.
 
The first phase involves it attacking your entire party with all four of its laser cannons, which are visibly mounted around the circumference of the machine. As you begin to hit it, you will begin to damage its cannons in sequence, eventually disabling them one by one.
 
After you've disabled all of its cannons, it will then attack you with a weapon called the "Smasher." This attack hits only one character but packs more punch than the attacks from the first phase of attack. Nevertheless, this is likely the easiest phase of the battle because it's impossible for the Arsenal to take out your entire party simultaneously.
 
Continue to wail on the thing, and the Arsenal will enter its final phase of attack during which it will release an incendiary spiral of projectiles. This attack is also called the "Smasher" though it bears little resemblance to the previous Smasher attack in both behavior and potency. The Smasher in this iteration hits all standing members of your party, and causes significantly more damage on average, per character, than both the previous Smasher and the arsenal's laser cannons from the first phase.
 
Out of Nowhere
The Arsenal is part of a seeming trend of final villains, notable in Square games but likely in many videogames (and other mediums), that  seem as if they come out of nowhere in relation to the rest of the story. In actuality, the real overarching threat in Final Fantasy Legend II is arguably Apollo, whose goal is to collect all the MAGI, abuse its power and achieve a much higher level of godhood for the purposes of power (as opposed to benevolence). It's almost certainly the resulting release from this abuse (when your party fights him, he explodes because he can't contain this power) that causes the security system to go berserk, and it's at this point where you first hear about the Arsenal--one dungeon before you go to confront it.
 
Of course, it's not as if the Arsenal is necessarily acting belligerently. It's implied that this is all a malfunction, and Isis makes it sound as if you're all heading down there to just pull the plug. Unless there's secret intent or evidence that the writers didn't give us, it's not as if Apollo is controlling the thing. It just kind of makes its appearance in the story at the final hour, out of nowhere.
 
Square in particular has pulled this measure off in a few of its other more "marquee" games, though arguably not as egregiously. In Final Fantasy III, for example, a "Cloud of Darkness" is responsible for trying to purge light from the world--but until the very last stanza of gameplay you're unaware of the nature of this thing. Instead you've been spending the last few hours chasing around a Warlock named Xande, only to defeat him and realize that he's not the ultimate enemy. Similarly, in Final Fantasy IV, the final villain Zemus suddenly undergoes a metamorphosis into Zeromus, the culmination of Zemus' hatred and darkness. Zeromus is never mentioned nor explained until literally the few minutes of dialogue before you have to fight him.