Hello, and welcome!
My apologies that you did not receive an earlier answer. Your patience is greatly appreciated.
I'm sorry you and your Toby find yourself in this difficult situation.
I just have a few questions to clarify some points.
You mentioned that your roommate has never had any pets, so Toby's aggression is toward YOUR female cat, whom he has lived with in the past and had no problem, correct?
From your description, it sounds like Toby is very stressed/upset about being in a new environment and is taking out his 'redirected aggression on his female furry companion and your housemate. This is not uncommon, when cats are stressed.
The first thing I would do is get some Feliway plug ins; these emit cat calming pheromones and should help the situation.
You can also add some Rescue Remedy for Pets to Toby's water. You need to reassure him all is well and surround him with his old, familiar items--cat bed, toys, scratching post or cat tree, same water and food
dishes (if you still have them), litterbox, etc. I would also add 1 more litterbox.
Try to enrich his environment and keep him occupied with some interactive and other toys:
Make sure to clean the counter and anywhere he soils, with an enzyme based cleaner, so he can no longer smell it and not return to that place, thinking it's okay to defecate there.
He's marking territory, which is instinctive and not uncommon, especially if he's an alpha cat.
If your roommate doesn't know how to handle cats, due to lack of experience, have him offer Toby healthy cat treats from his palm or just put it down in front of him. so he doesn't chance being scratched. To cats, food is love, and if he views your roommate as a source of food, he might no longer view him as a target of aggression.
Also, take one of your old t-shirts and rub it on Toby, your female and your roommate--even the counter, so he smells your familiar, comforting scent all the time, throughout the house and this will help him feel more secure.
If this behavior continues and nothing else helps, before you can move out, discuss with your vet, a prescription calming medication for Toby. I always like to suggest prescription medications as a last resort.
Another helpful product is a calming collar that contains pheromones like Feliway. Sentry Good Behavior collar is a good one and so is Nurturecalm. You can find these in pet supply stores or order online.
I hope things improve soon, for Toby and the entire household!
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