Omega Mk.II changes its elemental weakness as soon as it is hit by it, and has Auto-Reflect. Omega Mk.II is weak against Stop. Atomic Ray and Flamethrower are Fire-elemental attacks and thus can be absorbed with the correct equipment. Earthquake is a ground-based attack and will miss on floating targets. Remedy, used as a counter for Rapid Fire, heals Omega fully, unless it is used right after Omega Mk.II has used Search, in which case Omega Mk.II uses Remedy as a counter, not on itself, but on the character it has targeted.
Player should treat this fight as if they were facing the regular Omega, but should avoid using elemental attacks (via the aid of Spellblade) unless player knows what Omega Mk.II's weakness is. The player can use Flare with Spellblade freely as it's non-elemental magic. Due to the boss's Reflect status, the only way to know its weakness is to bounce Libra off a character with Reflect. Using the Dragon's Kiss Mix item on party members can also render most of Omega Mk.II's counter attacks useless.