Hello, Becca and welcome!
My name is XXXXX XXXXX it will be my pleasure to assist you today.
I'm sorry Ninja is not feeling well.
It's possible that the kitten brought an infection into the house, like an upper respiratory infection (kitty cold), which is not unusual, especially if you got him from a shelter or pet store.
From your description of his symptoms, it would difficult to say with any certainty what could be wrong, but possibilities could include a dental problem like an abscessed tooth, sores in the mouth, infected gums, something stuck in the mouth (check the roof of his mouth and under his tongue, back of tongue) causing the drooling, however, drooling can also be a sign of nausea so he may have an intestinal problem and this is causing him to be nauseated. Maybe he ate something he wasn't supposed to or he could be constipated and feels like he wants to throw up, hence the coughing. He may have a big hairball he can't get rid of.
The third eyelid showing, indicates general illness in the body and his low energy is of concern. Also, if you haven't seen him urinate today, he may have a urinary blockage, which is an emergency in male cats. You can read more HERE
It would be advisable to have him seen by a vet as soon as possible, to get a diagnosis and treatment, so he's feeling better soon. If he seems really poorly, you can bring him to an ER vet center now, if you are able. If you don't know any ER vet centers in your area, please let me know your city/state/zipcode and I will research them for you.
I hope all will be well with your Ninja! Also, try to keep him separated from the kitten, since you don't know what he has and don't want the kitten to get sick if Ninja is contagious.
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