Marill was first called upon in The Crystal Onix to help locate the mythical Crystal Onix using its superior hearing abilities after Tracey's Venonat failed to locate it with its sight. In a matter of seconds, Marill picked up on Onix's voice and led the group to its secret den located on the other side of Sunburst Island. As a Water Pokémon, it was also able to find Onix hiding underwater.
In Tracey Gets Bugged, Marill teamed up with Venonat on Murcott Island to help search for Bug-type Pokémon. Working together, they were able to locate an injured and elderly Scyther that Tracey was able to capture and help.
Tracey loaned Marill and Scyther to Misty to help fight a fire on Ascorbia Island while he went to search for Captain Aidan's missing Wartortle in The Pokémon Water War. It managed to help out long enough for Team Wartortle to come and take care of the rest.
On the day that Tracey announced that he would leave the group in order to be Professor Oak's assistant, he used Marill to help send Team Rocket blasting off after Scyther had rescued Pikachu from them.
Gold and Silver series
Marill later appeared and helped with the crisis at Professor Oak's laboratory in Bulbasaur... the Ambassador.
Advanced Generation series
Marill hasn't been seen much since Tracey arrived in Pallet Town. However, it produced the Egg that hatched into what would be Misty's Azurill. The two can be seen battling alongside each other in The Right Place and the Right Mime, firing dual Water Gun attacks at Team Rocket after they had tried to make off with the Pokémon at Professor Oak's Laboratory.