Shadowrun on the Genesis, it took me weeks of daily play to figure out how to get through the game's plot, with a lot of going on random runs and working stats. I nearly maxed out my stats by the time I gathered the courage to go explore the wilderness outside the city and further the plot, and then the story missions seemed to all quickly fall together and within a week I had reached the ending. I had spent so much time playing the game that I didn't want it to end, even though I loved the ending.
So I just replayed it. Ended up playing through Shadowrun like five or six times after that, getting the story down so it could be gotten through entirely, including doing side missions for cash and rep, to like four or five hours. I only stopped when I got a copy of Gunstar Heroes.