Is the D&D Pantheon as invincible as it appears?

Question

I've recently taking up the ill-advised task of skimming Deities and Demigods. Numerous times throughout this book, the idea of PCs killing off the gods is entertained. For example, page 31 says that a sufficiently high level Epic party may have an easy time defeating the deities in the book and page 220 has a section devoted to deicide.

I can see this being possible for some pantheons. Numerous members of the Asgardian pantheon are quite weak and almost all of them lack Alter Reality, the Olympian pantheon's Nike and Hercules stand out as targets (low Divine Rank and no Alter Reality), and you might have a shot at the weaker members of the Pharaonic pantheon (e.g. Imhotep is DR 1, lacks any instant-kills, and is level 20 Expert). For these cases, I can at least see what the designers were going for.

The thing is, I just don't think that this is possible if the DM is using the D&D Pantheon. With the sole exception of the web extension deity Erbin, every single deity in this pantheon has Alter Reality. In my opinion, even under a strict RAW reading of its benefits (i.e. the Notes section), anyone who has this Salient Divine Ability is invincible. I can't even see how another deity can kill them.

To support this point, this is how I envision a battle between anyone who has Alter Reality and anyone else:

1. Before the battle, the deity makes use of its immortality, access to any Divination spell it wants (via Alter Reality), and (usually high) intelligence score to access any of a number of exploits for moving first.
2. As soon as the deity becomes aware of a battle or an upcoming battle, the deity moves first and uses Alter Reality to cast Persistent Time Stop. It now has an entire day to prepare for the fight. If that's not enough, it casts it again and again until it is enough.
3. Given that the deity has Alter Reality, it can do pretty much anything to prepare for the battle. My favorite is dropping an arbitrarily high mass on top of the opponent, but I'm sure that the ability to create temporary magic objects is even more useful (scrolls, any one?). The only limitations are those listed in the rules for Time Stop.
4. The deity either wins as soon as Persistent Time Stop finishes, or has an eternity to prepare an escape plan. In other words, the deity can't lose.

With all of this available, how can anyone, PC or otherwise, manage to defeat a deity that has Alter Reality? I can't see how even Epic Spellcasting can overcome this. The only weakness that I can see is in antimagic fields, but deities largely ignore those anyway and have numerous options for countering them via Alter Reality. For example, Wish can destroy Dead Magic Zones, Mage’s Disjunction might be able to destroy the antimagic field without stopping the Persistent Time Stop, and Salient Divine Abilities explicitly ignore antimagic fields.

Answer 1

The question is too open-ended, so I'm only going to address the approach you spoke of in the body.

Your claim hinges on two core capabilities:

1. Going first.
2. Infinite Time Stop.

Going first

The answer you linked already addressed the majority of this topic - there is no universal "I go first" button, and from a TO perspective the only leg up deities have in this contest is access to the Supreme Initiative. It is admittedly a good leg up too, but not all deities as statted in Dieties and Demigods has it.

Let's say the deity uses every advantage it has, including Supreme Initiative and goes first.

Infinite Time Stop

If a deity is replicating the spell Time Stop via Alter Reality then it is subject to all effects that interact with that spell.

Two of those are notable:

1. Spell Stowaway
   This is an epic feat from the SRD that allows you to "hijack" a spell effect. In the case of Time Stop it brings you along within the casters Time Stop, effectively nullifying it.

2. The 5th spell Temporal Repair [Dragon #350, p.78]
   This is an area spell that prevents time-altering effects from affecting anyone within its area. For spells of its level or lower it works automatically. For higher level spells it requires passing an opposed caster level check. But there are many ways to boost caster level up the wazoo.

Both these approaches suffer from some serious limitations like their limited range among other things. But what we are looking for here is not a definite win, but simply removing the deity's "I win" button, making it a contest of planning, and resources, and "who has the higher number?" once again.