Gary is seen in SpongeBob's home at the start of the episode, but when Patrick falls down stairs in his home, Gary can be heard yelping.
The Krusty Krab would have been temporarily shut down as a result of the fungus as Squidward would have been at risk of infecting other customers.
Squidward grabs Spongebob's toy to fix it. While he grabs it, you can see Spongebob's mouth is closed, but you can still hear him crying.