I want to make a powerful spell that, regardless of equipment, would drain the users magic and render him unable to use magic for ...say.... a few minutes, even if that player has equipment that lowers magick cost by 100%. Is there any way to do that?

Sure, you could use a magic effect with a simple script attached to lower the player's Magicka and MagickaRate to zero (using http://www.creationkit.com/ModActorValue_-_Actor), then apply a hidden perk to them with an http://www.creationkit.com/Perk_Entry_Point that does something like Mod Spell Cost, and "set value" to 100, which will override any magicka cost reductions, and make their spells cost 100 magicka, which they will no longer have.

ok, I have to admit I haven't scripted for Skyrim before (only NV), so please bear with me. so I would write a script like

Game.GetPlayer().ModActorValue (Magicka, 0)Game.GetPlayer().ModActorValue (MagickaRate, 0)

and then attach that to a magic effect in the spell. Right? That way, after the spell is cast, it sets the players magick and magic regen to 0.

Then what kind of script do I use to apply that moded spell cost?