You've not been very specific about what actually happens. How did you end up getting a game over with no Pokémon? Does "no Pokémon" actually mean "they all fainted", or literally "a party length of zero"? Did you move from one map to a different one because of this, or did you stay on the same map? Was poisoning involved, or losing a battle?
In the map you return to (usually a Poké Centre interior), is there an autorun event which heals the player's party? It's generally the second page of the nurse's event, which depends on the "Starting over" switch being ON (the page turns it off again).