The entire song is about Isaac questioning free will. The opening line says that we often wonder (have thoughts) but it's no thing of wonder (as in a miracle). He is saying that the thoughts that pop in our head aren't miraculously being thought of consciously, but merely anecdotal based on our emotions and surroundings.
Another line: "with great tunnel vision, we built ourselves a mission to ride out motives design." Tunnel vision refers to how narrow our set of goals are, given our interests and experiences. For example, if you know yourself pretty well and your biggest interest and passion is music and you have always played the drums, odds are you are going to play the drums, not be a surgeon. We have a narrow set of goals, we create a mission to achieve those goals, and we follow the design of our motives.
Another line: "I wasn't always cargo, I was once kinda my own. I guess I'll pack up my mind." This refers to himself coming to understand the delusion of free will. Here is why. Cargo does't have a choice on where it's going. Based on what's inside the package, it will go to whatever place that needs the cargo. He feels that he is the same way. But, he says he wasn't always cargo. This means he previously had thought that he was in control of all the decisions he made and where he was going. But now that he knows he is just cargo, he has no choice but to "pack up his mind" and go wherever he was always going to go.