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Say I flip over Holy Grail and use it.  If my opponent plays DoN immediately does his character go back to being an Evil Character?

Holy Grail
Type: Artifact • Brigade: None • Ability: None • Class: None • Special Ability: Holder may convert one human Evil Character per turn into a Hero in the brigade color of Holder's choice. Holder is limited to two such conversions per game. • Errata: Holder may convert a human Evil Character in a territory to a Hero in brigade of holder's choice once per turn. May be used twice per game. • Identifiers: None • Verse: Matthew 26:27-28 • Availability: Warriors booster packs (Rare)

You can negate the first use of Holy Grail during the phase in which it is used.  If you wait until a later phase, the convert is not undone.

Isn't it true that when you activate (flip it over) any artifact the opponent(s) have a right to play DoN before it is used or do the opponents have to wait to play DoN until its s/a is done?

You can use the instant ability of an Artifact as soon as you flip it over, before DoN, assuming conditions are met for it. Which is why Urim and Thummim is just about impossible to get rid of, unless you get lucky with the RoA characters who can discard a face down art. What you can't do is activate an Artifact which is ongoing (like HoH) and immediately enter battle to prevent your opponent from being able to "negate" it for the battle phase. You have to give your opponent a chance to respond to the activation first.