Some grad applications have a special circumstances portion that allows you to make note of any issues with grades. Say there were semesters where you were having medical problems or you didn't have access to services and your GPA suffered from that. Also, you can make note of it in the statement that you write for grad school as well, if they don't have a special circumstances portion.

You could talk to the academic counselor at your school about this issue as well and they might be able to help you. I talked to my counselor about it years ago amd we discussed this option.