Can anyone explain how to use MPL sensor with Arduino MEGA?
Since the device is 3.3V and the Arduino is 5V, you will need a I2C level converter such as the TCA9517. Simply supply the Mega side with 5V and the device side with 3.3V and attach 4.7kohm pull-ups to 5V on the Mega side, and it will convert both SDA and SCL for you. You won't need pull-ups on the device side since it includes pull-ups on the board.

For I1 and I2 (push-pull outputs) you can use either normal level converters or you can use a SN74LVC2G07 along with the pull-ups found on the Mega inputs.