She appears much earlier as Aya Brea's clone, Eve Brea, and appears as a normal girl before being consumed and transformed. In her human form (which she reverts to) can control the ANMCs and, indirectly, is responsible for the events in Parasite Eve II.
Being the final fight in the game, Eve is fairly difficult and Aya should not hold back. After she is defeated, Eve grabs Aya and falls to the bottom of the shaft. In the end, Eve is completely destroyed as both Aya and Eve Brea are found alive and well.
Hopefully, Aya has Ringer Solutions left from the fight with the previous boss battle and it's important to make sure that there's enough ammo to make it through the fight. With a good armor with HP Recovery, Aya should have full HP and MP for this battle and this is extremely important. Without this, it may be useful to use Healing to get her back to max, then upgrade a PE ability to max out MP again.
In terms of weapons, the M203 is not that useful as her agility makes her fairly hard to hit. Energy Shot 3 is very useful. R. Slugs, if you have them, can be good, and the M249 with Energy Shot 3 can deal 1000 to 2000 damage with half a magazine. Just go all out, try to avoid her attacks and everything should be fine.
Eve's appearance is similar to her first incarnations, although she looks much more inhuman and possesses a very different attack style. Mainly, Eve will fly around the room moving through portals in an attempt to hit Aya with a dash attack. If Aya runs onto the bridge, Eve will perform a devastating slam attack.
After she performs this attack several times, Eve will appear above the bridge and surround herself with an Antibody glow (decreased damage, only for a very short while).
Occasionally, Eve will flood the room with Mitochondria clusters that will replenish Aya's MP counter, but Eve isn't being generous, she's trying to flash the Mitochondria with liquefying heat, especially those stored in Aya's body. Attacking and interrupting her yields the benefits: a slight MP replenish, and extra damage dealt.
If you have Apobiosis level 3, it will be an easy fight since you can stun her, leaving her completely vulnerable (except the moment when she uses the dash attack).
Eve can be poisoned via Necrosis or the "Maeda" magnum rounds, and if Pyrokinesis or Grenades are used enough, Eve's lower half will split, dealing heavy bonus damage. A good tactic is to couple these effects.
When she is reduced to about half her health, Eve's attack pattern takes a turn for the worst, she has two new attacks, both of which can be very dangerous: the first attack are three homing energy spheres that can be hard to dodge and they inflict status ailments such as Berserker; with the second one she can summon a ghost which can deal great damage to Aya and cause status ailments as well, this ghost can and should be destroyed as soon as possible.