What if....... what if Artemis's father is actually a fairy?
Why else would he disappear so often?
Why else would Artemis's mom be so calm about the fact that Artemis has been hanging around with fairies on dangerous missions?
I have a feeling that she's always known something, and that Artemis Fowl Senior has mind wiped her in the past, but thanks to Opal's moment when she took over her body, her memories returned because of her contact with magic and all of the familiar images and moments.
I think Artemis is the first Fairy/human hybrid and that explains his vast intelligence and ability to store magic- AND MANIPULATE IT.
Don't you guys see? HE IS A FAIRY! He belongs with Holly.