Self Surrender to the nearest immigration center for repatriation back to home country.
For overstaying, you need to have a EXIT PASS Special Pass in order to exit Malaysian Immigration checkpoint.
A Malaysian Visa is just to enter only.
You will have to pay overstay fines and a blacklist for any re-entry.
Further Notes :
What should I need to do after my Malaysia EP visa have expired for 3 months? I have overstayed for 3 months. How much do I need to pay for Fine? Which process do I need to proceed to return to my country?
https://www.quora.com/What-should-I-need-to-do-after-my-Malaysia-EP-visa-have-expired-for-3-months-I-have-overstayed-for-3-months-How-much-do-I-need-to-pay-for-Fine-Which-process-do-I-need-to-proceed-to-return-to-my-country
What should I need to proceed for my visa process to return to my country after my Malaysian EP visa has expired and I have overstayed for 3 months?
https://www.quora.com/What-should-I-need-to-proceed-for-my-visa-process-to-return-to-my-country-after-my-Malaysian-EP-visa-has-expired-and-I-have-overstayed-for-3-months
Is the back-for-good program still available in Malaysia? If no, then is there any program for people who overstayed in Malaysia and wanted to go back for good?
https://www.quora.com/Is-the-back-for-good-program-still-available-in-Malaysia-If-no-then-is-there-any-program-for-people-who-overstayed-in-Malaysia-and-wanted-to-go-back-for-good
If your passport has been lost or stolen and you don't have an ID card with you, is it possible to get a new passport?
https://www.quora.com/If-your-passport-has-been-lost-or-stolen-and-you-dont-have-an-ID-card-with-you-is-it-possible-to-get-a-new-passport