Our senior cat has been very good about using his litter box to do his business, there was the odd time that he didn't and in the summer he used to go outdoors for that. Now he's gotten so he doesn't want to go out, even though it is getting colder he sometimes would still go out looking for either grass or to do business.
Our other cat, another male at a year and two months was run over about a month ago and he was a very hyper cat. Always pouncing and biting our senior cat, Yoda, every chance he got. Yoda had a hard year and seemed to be stressed a lot but would still use his litter box when he had to.
Now we have a kitten, it is female and Pocket is a good girl, she leaves Yoda alone most of the times but does want to play with him every now and then. We have two litter boxes set up right now, Pocket will use both but she has a tendency not to cover up her leavings, though she did when I first brought her home but now doesn't and I'm not sure why nor how to get her to start doing it. Yoda uses both litter boxes as well as far as I know to poop but lately he has a terrible habit of peeing in places all over our basement instead of the litter box.
I was wondering if it has something to do with Pocket, if he doesn't like her smell or that she doesn't cover her leavings up or is it that he is just getting old, he's around 14, and he mind isn't working correctly in this department anymore.

He sounds as if he is too old for change and although there was dissention with your cat that died, probably missing him in the house. It could be one or two reasons. Can you move his litter box away from your new kitten's box? There isn't much you can do to change his ways now.

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