The State of Indiana requires that both partners be present when obtaining a marriage license. Both parties must provide a government issued ID to prove who they are and swear in front of the information provided on the marriage license application is correct and sign the license.
There are a few exceptions. Each county had different procedures and interpretations of the law. Marion and Hamilton County both have virtual appointment options. You both have to be on the same video call with the clerk but you can call in from different locations. After your virtual appointment, the clerk can either mail you the marriage license or it can be picked up. In this case, you don't have to pick it up together.
If one of the partners applying for the marriage license is incarcerated, some counties have procedures in place for obtaining a marriage license. You will have to contact your clerk directly. Most clerks do not - but it doesn't hurt to ask. Marion County DOES have this option. You need to be a Marion County Resident to obtain your marriage license in Marion County. Johnson and Hendricks Counties DO NOT.