Kogoro dies trying to protect Conan at the end of the Okiya Subaru arc. The FBI immediately afterwards are able to help stop the BO (BO are the ones who shot Kogoro). Kogoro says a lot to Conan as his is rushed to a hospital by the FBI and once Ran and Eri are there he keeps Conan's secret (which he knows, considering he was shot by the BO) while keeping everything a secret (to protect Ran) but tries to be father-like towards Ran and apologize to Eri. And then he dies. It was too late.
Conan and Ran now live with Eri. For the next arc you can have Ran and Eri try to figure out Kogoro's death while Conan tries to figure out what to do after this tragedy and all of Ran's sadness and confusion. Kaito Kid can be the new character who will help in the fight against the BO, with him wanting to help because of both losing "dads" (Kid probably wouldn't know it isn't his dad) to this organization (or organizations?). And we continue from there.


Kogoro was an integral part of the anime series for nearly 14 years now, it's not the same with him talking in a different voice.



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