For 2022, you should have reported the excess and paid a penalty on form 5329. If not you need to file an amended return.
For 2023, you should have reported the combined excess and paid a penalty on form 5329. If not you need to file an amended return.
For 2024, were you eligible to make contributions, and did you make any?
If you were not eligible in 2024, you need to pay the 6% penalty on your 2024 return using form 5329, then skip to the next section.
If you were eligible in 2024, then you can apply some or all of the 2022 and 2023 excess to your 2024 limit. For example, suppose the excess was $3000 for 2022 and 2023 ($6000 total). Your limit for 2024 would be $7000, but if you contributed $1000 or less, you could apply the 2022 and 2023 excess against the 2024 limit. If you already contributed more than $1000 (in this example) you could remove the 2024 excess by the special procedure, even though it is too late to remove the 2022 and 2023 excess by the special procedure.
If you still have an excess after filing your 2024 return, then to remove it in 2025, you just make a regular withdrawal of the excess amount. This will be an "early" withdrawal under the regulations. However, withdrawals of your Roth IRA contributions are always tax free, and withdrawals are always in the order of contributions first, conversions second, and earnings last. (If you withdraw earnings, that is subject to regular tax plus 10% penalty.) As long as your total lifetime contributions (minus any prior withdrawals) is more than the amount of excess you need to withdraw, then the withdrawal will be treated as a withdrawal of contributions and will not be taxed. And, there is no difference in whether you do that now or December, so you might as well put the money back into investments if you think you can earn something in the mean time.
This is just a standard withdrawal, no special procedure is needed. The IRA custodian will code it as an early withdrawal because that's all they know. The details will get worked out on your 2025 form 5329. You self-certify that you are withdrawing contributions and not earnings. The IRS theoretically has the ability to double-check by looking at your record of contributions from the form 5498 they get, or if audited, you would show copies of form 5498 from various years to document that you are withdrawing contributions and not earnings.
