For Init-drivers, if any of the peripheral's interrupt request sources are enabled, a skeleton ISR is inserted into the file driver_isr.c. The user will have to add his own code into this skeleton ISR.
Note that in order to insert the skeleton ISR into driver_isr.c, the option "Include ISR harness in driver_isr.c" must be selected in the Init driver settings in Atmel START. This allows the user to use an Init driver but to place the ISR in the file of his choosing.
Peripheral drivers such as USART Basic implements their ISRs in the file <DRIVER_NAME>.c, e.g. usart_basic.c.
Many Foundation Services drivers using ISRs allow the user to hookup callback routines to the default ISRs. This allows the user to have the ISR perform user-specified behavior without having to modify the ISR code itself.