Bodily autonomy. It's a term that has essentially lost all meaning in our culture today. Not because it doesn't have an objective meaning, but because the cry for "bodily autonomy" (e.g. "my body, my choice") has been accepted uncritically as a modern slogan, despite most pro-choice people being unable to defend the proposition that bodily autonomy justifies abortion. Pro-choice people assume (through repetition, usually without argument) that the child's dependency upon the mother and location inside her body gives her the moral right to have the child killed. But in absolutely no other context can I use my right to bodily autonomy, ipso facto, to justify killing someone, nor does someone else's dependency upon me give me the right to kill them. It's usually quite the opposite: if someone is dependent on me for survival, and I must use my body to help them, it gives me a greater obligation to help them.
Immanuel Kant was an agnostic philosopher. Notably, he rejected Realism (which I hold to), but even so I believe he offered valuable insight. Kant argued that we are rational agents, and as such morals must be grounded in reason alone. He was one of the earliest philosophers (that I'm aware of) to speak in terms of autonomy. Kant argued that we should follow what he calls the principle of autonomy (auto-nomos, which means "self-legislating). As R. Scott Smith, in his book In Search of Moral Knowledge: Overcoming the Fact-Value Dichtomy (InterVarsity Press, Downers Grove, IL, 2014, p.94), wrote:
In our context, 'autonomy' often implies that each person decides what is right for him or her. Clearly, though, Kant was not a relativist. For him, we are to be self-legislating and develop maxims, or plans of action, that are to command us categorically. Moreover, we are to will to universalize them. Thus, they are binding independently of our desires, consequences or other experiences. By acting autonomously, we do our duty for duty's sake, out of pure respect for the moral law.Again, Kant was not a relativist. Since we are rational agents, that means that we are bound to the moral law. Rational agents are intrinsically valuable, meaning they are valuable in and of themselves. Another way of saying this is that they are an end unto themselves. So one of our duties is that we are never to treat other rational agents as purely a means to an end (in other words, as purely a means to get something else that we desire). They are always to be treated as an end, themselves. This means that all human beings have human dignity. Abortion treats the unborn as a means to an end, not an end unto themselves. This means that if you really do hold to bodily autonomy, you should also hold that abortion is immoral. Having bodily autonomy means you have the right to follow your duty as a rational agent, not that you have the right to do whatever you want regardless of how it affects other people.
The next time someone talks about how bodily autonomy justifies, remind them that while bodily autonomy is very important, there are limitations to it, just like there are limitations to most of our rights.