First is their a tardy policy at your school? If there is you might want to make sure they follow that prior to letting them in.
I say this only because that later becomes part of the one to one. After your class is working, walk over to the student and ask if you can see them (right outside your door) I often refer to this as 'my office'.
I would begin by acknowledging that you noticed that they are often late, yet they come and you are happy to see that they do come.Is everything alright with them? with their home life?
What would it take , what kind of support can I offer for you to get to class on time?
Now the class is doing ______________________(repeat assignment) do you need any help? you can come see me. (when)________ or I can help jump start it now (If that's possible)
If the student responds in the negative they do not need help they are okay , then transition into the fact coming to class and not participating guarantees them a F. Make-up (if you do make-up) is only for students who are sick or other unusual circumstance. Let them know that you really don't want to fail any student. "So please let me know how I can help"
Go find out what their current academic status is they may be failing academically and just feel hopeless. If this is it, refer if you feel more comfortable. If you are up to it help them discover options. What is their passion? (If they could do anything what would that be? (They do not have to know) What do they do in their free time? Refer to counselor or appropriate person. Good luck and thank you for caring enough to ask. Together we can make a difference.