My wife is re-enlisting for a bonus. If she becomes pregnant and leaves the Army she will have to repay part of the bonus she is receiving. My question: How would the repayment to the Army handled? Do we repay one lump sum or on a payment plan? How are taxes handled in regard to the repayment? (We would have to submit an amended 1040). Thanks.

If your wife is chapter out of the military for pregnancy, she will have to pay that bonus back.

The government will get their money, i.e., final paycheck, tax returns over a number of years, etc ....

Why are you are your wife considering reenlisting and/or getting chaptered in the same thought?