How does one alter the missile effects to show a spell effect or alternate explosion upon detonation?

The missile itself needs the necessary unit graphics, but what specifically needs to be altered for say, a gas cloud for an explosion?

Also, is this limited to 2 missiles graphics only (nuke & general missiles)?

It's the death animation.

I already looked at the cruise missile death & the nuke deaths. None are the in-game graphics.

\Civilization III\Conquests\Art\Animations?

That's where you'll find the misc ones.

Miscellaneous graphics are like fireworks, bombing runs, rioting, etc.

The missile detonations are not there either (chekced that too). That's why I made this thread - none of the obvious places have it.

Got it, I ctrl+f'd the civ3 folder for *.flc, and in "\Civilization III\Art\units\Cruise Missile" it is. "CruiseMissileDeath.flc" is the name of it.

EDIT: Ie Aaglo was correct and you didn't look hard enough.

Found it. The Death flic is used for destroying a missile. Nukes (but not cruise missiles) also have a Bomb flic which is used as the Death animation (in the .ini file).

So a nuke explosion can be altered, but if a cruise missile is a bombardment - can that have an animation? It normally doesn't - or if it does, it may be a small default bombardment animation - maybe the bombing run flic?

"CruiseMissileDeath.flc"

EDIT: Ie Aaglo was correct and you didn't look hard enough.
That's the animation for when you destroy the missile. You can confirm that by viewing the Nuke death - which is clearly not the Nuclear mushroom cloud.

The death.flc is used with cruise missiles (exemple the gas cloud effect is on the DEATH= -row.)

I don't know about the nukes. Look at the nuke ini-file, and see what line refers to the mushroom cloud.