There is a legend that the God of Flames, God of Freezing, and the God of Thunder should not be disturbed or else the Heavens and Earth will become angry and wreak havoc on the planet.  Only the God of the Sea can qualm their anger and restore peace to the planet.  Jirarudan, a Pokemon Collector, believes in the legend and decides to capture all three of the bird pokemon to bring out Lugia, the God of Water.  He succeeds in capturing Fire (the God of Flames) and goes after the other two (Freezer and Thunder, the God of Freezing and the God of Thunder, respectively). 

Satoshi crash-lands on the island chain where the Pokemon Gods are said to reside and is asked to go to the islands of Flames, Thunder, and Freeze to get small orb-like gems that'll calm the gods' angers and keep balance in the world.  Satoshi gets the treasures of Freeze and Thunder before meeting Freezer and Thunder, who are arguing over who should get Fire's territory.  Jirarudan arrives to claim Thunder, and in the process he captures Satoshi-tachi as well.  The pokemon trainers are soon released and eventually succeed in freeing both Fire and Thunder.  The three Pokemon Gods, having been brought to the same location, begin to fight. 

Satoshi and the others sleep as their pokemon have an adventure.  Togepi goes exploring after a Ledyba when it gets lost in a pokemon valley.  The other pokemon follow it into the valley, led by Elekid, where they are entertained by various pokemon.  They're side-tracked for short while, but soon get back on the trail to rescue the little egg pokemon.  A big storm comes as the pokemon struggle to hold on to the nest that Togepi's in, but by working together they're able to keep the egg pokemon safe. 

The Ancient Myuu card

From left:  Japanese VHS, feature; Japanese VHS, mini-movie; 
American VHS, main feature + mini-movie

From left:  Japanese DVD; American DVD

Thanks to Pokemonica for the above staff list.