Company is threatening ex-employee

I was working with a company 3 months back. They told me one day that my performance is bad and I have to leave the company. But company will pay me 1 month salary and the last month salary for the days I worked. Also, when I joined the company I took a joining bonus amount which I was supposed to return if I leave the company before 2 years. Since they asked me to leave before 2 years, I asked them to waive off my joining bonus recovery. HR agreed to it and told me that I should take Manager's approval for this. My manager approved this. And they told me that I can collect my settlement amount after 45 days. They also told me to write a resignation letter on the same day. After 45 days, they told me to come after 2 weeks as my case is complicated. I called them again after 2 weeks and they told me to come and collect the cheque. When I went there, I asked them why they deducted my joining bonus amount. To which they said, it\'s company policy and they cannot change it. Now they sent me a notice that I took the letter illegaly from them and I threatened them. But I didn't do anything. Infact, I was just asking them a logical explanation for this. They also wrote to me that they will file a police complaint against me. What should I do now?