Kinda depends on what ending is canon. But I guess you could resurrect him by accident. Some rival corp, looking to find the secrets of Soulkiller resurrects his engram. The information wanted, is wrapped up in Silverhand himself. From there you could either go, nerd smuggles Johnny out and its a cat and mouse game with all the corps trying to find the soulkiller code, and Johnny. Or you could insert Johnny into the city, working behind the scenes to take down all the corps. And you, as some random, is who he chooses to give assignments to in order to take them down.

Maybe If I give it more thought, but off the top of my head, thats what I came up with. So bringing him back is totally doable without feeling contrived.