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Be sure to search all the bodies as well as the flesh pods along the way because you will find a bunch of crystals that you can use to activate powers that will help you defeat The Mother. As you descend into her underground lair, you’ll come upon three different socketed circles where you need to place the crystals. They are found at the bottom of the giant spiral stairs. If you have enough crystals, click on each socket to place them. Four crystals are needed to activate the power of this magic circle. You may have to back track a little to activate some circles, but it’s worth the benefits you gain.
Take your time to gather up all the crystals to activate the magic circles, and this will help during the battle. You’ll get a little diagram that appears in the upper right corner of the screen, and this is used to activate the powers granted by the magic circles. One of them launches a huge firestorm down on The Mother and her minions. Another heals up your whole party at once, and you’ll definitely need that as the fight goes on. The third lets you stun everything in the area, and this you can use when there gets to be too many at once.
At some point, The Architect will offer to help you defeat The Mother, and you should accept its offer. With its help, you will get one more giant fire spell that does even more damage.