My cat is suddenly aggressive! :(

So recently, I started treating my cat for bartonella, which is tested strongly positive for. He's already getting better, but since my fiancee and I started giving him the meds, he's become reclusive, and yesterday he acted out towards my fiancee, hissing and scratching him. Luckily, he's no longer contagious, because this could have been very dangerous! I just want to know if anyone has any ideas of what I could do to 1. Get him to come out from under the bed and 2. Reverse, or at least lessen his aggressive behavior towards my fiancee and my other cat.

Call your vet and let him/her know what is happening.

What kind of medicine is it? Pills, liquid?
Cats usually hate medicine, and some of them can get "traumatized" from taking it, and get recluse, which I think it is what is happening with your kitty. My Bugsy is like that. Unfortunately it will take a few days after you stop giving the meds for him to get back to normal. The way around that, is to find a pleasant way to give meds: If it is a pill, try to insert it in a pill pocket, or in between two soft treats. If it is liquid, try to mix it with his wet food, or with tuna, or tuna juice, or clam juice.

For Bugsy, what works the best is to mix it with his wet food.
If the pill pocket doesn't work, ask your vet if you can crush the pill and mix it with food - this also works well with Bugsy.
Also make sure to praise him bunches, and give him treats every time you give him meds.
To take him out ofthe bed, try to lure him with treats. Make sure to do this throughout the day, to play, to cuddle, so he doesn't associate getting off the bed and medicine.
How many more days do you need to give him meds?