Now, this is just a minor theory I came up with, based on the theme of the album (all things mathematical, physical, and I'm gonna go out on a limb here and say quantum), to speculate what happens with The Father in the final scenes of The Theory of Everything.
Now as we know, after being left by The Mother, The Father is grief-stricken and concludes there is only one thing left to do. What we know is that we eventually learn about his suicide, so this was probably the conclusion he drew. But we also know that The Prodigy actually saw his father and completed The Theory of Everything with him. And essentially, apart from the fact that The Teacher was the only one who knew where The Prodigy was hiding (which is a major hole in my theory, I have to admit, but I digress), there's no reason to assume the possibility of his final conclusion being "I'm going to find my son and complete The Theory of Everything with him, since I've literally sacrificed everything dear to me to get there" isn't an equally valid conclusion.
So what do we get from this? Until observed, we don't know what choice The Father made. Basically, he's Schrödinger's Cat, both dead and alive at the same time, but then more like Schrödinger's Mathematician! The wave-function does not collapse until observed (and although The Mother already found his lifeless body the night before, so there's another major gap here, I'm still going to entertain the thought), and he's both dead and alive at the same time. The Prodigy, influenced by the drug and his special mind that's able to see beyond the physical realm, may be able to observe this alternate reality, this parallel dimension in which his father made the other choice and found him. He basically channels The Father in his visionary/delusional/psychotic state of mind, and completes both his parts and his father's parts, using both his own handstyle and his father's.
Compared to the only other possiblity I came up with to explain The Blackboard (Reprise), which is that The Prodigy completely internalised his father's personality and was able to predict what his father would've come up with, emulate and reproduce his work and in that matter also channel his father (of course, also in a delusional state), well let's say I find the alternative more entertaining.
Let me know what you think! I spent way too much time thinking about this already!