You will have to complete an Indiana Nonresident income tax return in addition to a Michigan Resident income tax return. Michigan and Indiana are Reciprocal States. You should submit Form WH-47 to your employer so they stop taking Indiana income taxes and withhold Michigan income taxes.
A reciprocal agreement, also called reciprocity, is an agreement between two states that allows residents of one state to request exemption from tax withholding in the other (reciprocal) state. This can save you the trouble of having to file multiple state returns.
To file your Nonresident Indiana income tax return, click on How do I file a nonresident state return?
Additional information: Which states have reciprocal agreements?
