There are several theories on how the universe might end by time stopping. The problem with cosmology and some other parts of theoretical physics is that it cannot be proven, nor reproduced or tested. This makes it often more a faith/religion than a science. So, if you notice some irony in my answer, please, it's because of this.
There are two types of theories which fantasize about the end of the universe by end of times. I freely call those type the formula type and transcendental type theories.
The first theory I will only briefly describe, because they end up transcendental anyway. There are several models on the universe that will describe what the universe (or universes) looks like and how they will evolve in time. The problem with these models is the variable time. If you have an endless time or an endless amount of universes, you end up with an endless amount of possibilities, which will result in all things will eventually happen. So, somewhere in time or a universe we will all become filthy rich and marry a gorgeous, intelligent, funny, friendly, etc., woman/man that never says no (to you). Because of this anomaly scientists have started to theorize that time must end at some point. If you believe these models to be correct, the scientists might be right. The problem in this lies that you first must believe the model is right.
The transcendental theories are a bit more difficult to explain and I will briefly leap out of astronomy into philosophy. In the 18th century a great philosopher wrote a book on the critique of pure reason (Kritik der reinen Vernunft). In this book he was looking for a transcendental doctrine of method and elements. The transcendental part of his doctrine was that it had to be build up on a priori knowledge that was not based on experience. This was his pure reason, because the elements and the methods are not tainted by (personal) experience from an observer. They are true in itself.
Why is this interesting? Because Kant (that great philosopher) said that there were two transcendental elements, space and time. I will skip space, but must say something on time, because someone thinks it might end. Kant states that time is an a priori element of knowledge in pure form. Kant uses five reasons, why time is universal and not empirical. They all can be brought back to the fact that we cannot see things/phenomena to coexist together or successively when there is no concept of time. Therefore, time is an a priori element of pure form.
Now, what has this to do with the ending of the universe in respect to time? The theory you mentioned as heat death is such a transcendental theory. The theory states that the universe expands until the universe is too big to be heated by the energy provided by the matter in the universe. This theory models that the universe follow the same rules as any thermo dynamic system and therefore at a certain point in time all energy, matter and temperature are evenly distributed in this huge universe. Because all is evenly distributed no stars will be created and all processes come to a grinding halt. Since the state before, now and after are the same, the scientists now determine this as the end of time. The formula theories also end up making some theory that time will end.
The problem with these theories is that time will never end. According to Kant time is an a priori element of pure reason and will be there despite of what we observe. Because the state of the universe doesn't change, doesn't mean that there will be no time. Time has just stopped. Theories that state that time will end, do not comply with Kant's critique of pure reason, which states that time is the formal condition of all phenomena whatsoever.
If it didn't entirely answered your question, I hope it was entertaining and educational.
Kind regards,
MacUserT