Thank you for trusting your question to JA today. I am a licensed attorney with over a decade of law practice and over 20 years of experience in the legal field. I’m happy to be of assistance.
In employment law, unless you have an employment contract that expressly states you can only be terminated for cause, you can legally be terminated at any time with or without cause. This is called "at will" employment. So, the feeling that you have that your employer may want to get rid of you may be very accurate and, unfortunately, it would probably be possible and legal, unless you could show that the employer is actually motivated by discrimination against your race, religion, gender, age, disability or recent FMLA (medical leave) use.
Now, as to the unpaid stipend, if that was part of your pay agreement and you are not receiving it, there could be a way to protect your employment and try to get that given to you. Asking your employer for compensation that you are legally entitled to is a protected activity, so while your employer could be upset about it, retaliating against you for asking would be illegal. So, while I understand the concern about asking for the owed funds as a means of causing retaliation, it actually gives you some legal protection because any "adverse employment action" like a termination that immediately follows your request looks like retaliation, something your state level Department of Labor would take very seriously.
So, if you have not made a request to the employer, do so. If you fear doing so, then go straight to your Department of Labor and file a "wage claim" based on unpaid stipends.
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