How to kill a greater deity with Alter Reality and without using Pun-Pun or Ice Assassin Divine Rank shenanigans.
Do not even think of attacking him until after everything else in the following plan has been done. Attacking a god is going to trigger his portfolio sense. That gives him advance warning, and you will not succeed if the god has advance warning.
Becoming utterly immortal and unkillable:
Step 1: Have the Epic feat Ignore Material Components.
Step 2: Create an Ice Assassin of a Mind Flayer Psion (telepath) with a level greater than your own and physical ability scores in the 70s or so.
Step 3: Order the Ice Assassin to True Mind Switch with you.
Step 4: Kill your Ice Assassin.
Step 5: Gain 10 levels in the Illithid Savant prestige class.
Step 8: Create an Ice Assassin of an Aleax of yourself.
Step 9: Order it to shapechange into a form with a brain.
Step 10: Consume it's brain and gain the Ex ability Singular Enemy.
Step 11: Create an Ice Assassin of an Aleax Mind Flayer Psion (Telepath) of a level higher than your own with true mind switch and whatever physical abilities you want.
Step 12: Order it to True Mind Switch with you.
Congratulations, you now currently have two copies of the Singular Enemy ability each with a different singular enemy (one of which is yourself). This means that nothing in the multiverse can harm you in any way.
Now it's time to get you a whole host of abilities and qualities. This basically means using the Ice Assassin trick to produce brains of yourself to consume to multiply your abilities and brains of other creatures and characters so that you get every ability that is even remotely useful in the entire game. Once you have done that it's time to make use of Epic Casting.
What you do is create an Origin of the Species spell (using Ice Assassins to mitigate the DC down) with every epic ability as an Ex that you can conceive of (multiple separate creatures so that the DC doesn't get too insane) that are utterly loyal to you and then consume their brains to gain those abilities.
Now, you should consume the brain of a Vecna Blooded creature every day so that you acquire an updated the Cloak of Mysteries (Su) ability; the ability only hides all knowledge of you up to the time you gain the ability so you need to keep getting a new copy to keep your plans and actions mostly hidden. It still doesn't keep you safe from Portfolio sense but it does make you safer.
Now, one of the Origin of the Species creations of yours should have an Ex ability based on an epic spell with a free action casting time that uses the Contact and Transport seeds (along with hideously boosted saving throw requirements) to locate anyone or anything that you are familiar with and then transport them to any location that you are familiar with (make sure that it is capable of extraplanar transport and does not use the Astral plane).
Another spell choice should be a Ward spell that excludes all spells of up to say level 10 with a radius of a hundred miles or so.
The last epic spell choice you need to include is an area of effect dispel based on the Dispel seed with a radius around you of 100 miles when activated. Make sure that the CL check is boosted to an absurd level and that this is also an Ex ability for your target creature.
Then travel to within a hundred miles of the Spire in the Outlands. Spend the next 20 weeks there. Use your Ex Ward ability to shut down magic in the area. Use your Ex Dispel ability to suppress magic items until you turn it off. Use your Ex teleport ability to rip Nerull to your location, this strips him of all his divine abilities, blocks the casting of all other spells/powers, and shuts down all of his magic items including artifacts.
Now you beat him to death, or use another Epic Ex ability to kill him. This shouldn't be difficult considering that you have had 20 weeks to prepare the battlefield, have every ability in the game, and can't be harmed.
Congratulations, you killed an overdeity. Granted, the above plan will allow you to kill anything short of the Lady of Pain and it utterly abuses the Illithid Savant but it is RAW legal, doesn't require DM adjudication, and works.