Communication between three atmega controller
You could program another micro to sample both pins and send you information about the signal.
For instance, use input capture inputs of an appropriate Arduino board to determine the pulse lengths over a certain time, store them into a buffer and transmit that buffer via UART to your PC, where you can do an offline analysis.
Take care that your micro is powerful enough to handle the max. I2C frequency of 400kHz.
And make sure you have a good ground connection between both systems.