Machia refers to Afo as the Master[shyu] and Tomura as the Successor [koukei].
After Tomura defeated ReDestro and was sworn allegiance, Machia finally recognizes Tomura as the Successor [koukei] of Afo.
And many chapters later, Machia again calls Tomura - the Crown Master [koukei no shyu].
That time... the Crown Master... had Afo’s “smell” and “voice”! I know it!! It was undoubtedly “you”!!
For Machia, there is only one Master, and that is Afo.
Tomura was on the verge of death when Miruko broke the tank. He was literally dead, until a pure accident - a current discharge from a severed live cable - started his heart.
Two things happen at this time: 1 - Tomura consciously walks toward the vestiges of Afo, choosing his path. And Afo begins to consume him. 2 - Machia smells his Master and stands up to his full height in the shelter.
In doing so, Tomura begins to smell like Afo, like the Master. And Machia believes that it is Afo in Jaku, despite the fact that Tomura gives him the order over the radio.
Then, as Machia runs through the Osaka Prefecture, he smells the second Master.
Two things happen at this point: 1 - Izuku fully awakens the Danger Sense by attacking Tomura. 2 - Afo has already swapped places with Tomura in body control. However, he seems overly content because Izuku is hooked and has approached him himself - which means it will be easier to steal the OFA.
Many people think that just the Afo phenomenon in Tomura is the two Smells, but there are a few nuances here.
1. Tomura smells like Afo because it now has the DNA of Afo to hold the quirk AFO. Therefore, it is now THEIR smell as long as Tomura will have the Afo quirk factor.
2. The second smell is shown less than the first, and Machia could only smell it halfway to Jaku. And since smell is a physical thing after all, it can't come from nowhere, so this smell has always been there. And it must be weak enough that Machia couldn't smell it immediately 80km away in Gunga. Therefore, there must be a second carrier of the second scent.
3. Now we know that Machia noticed that the Master's successor, Tomura, had the smell and even the Master's voice in Jaku. Which suggests that these smells are identical and smell with the same intensity. Machia could not distinguish them until he arrived in Jaku and looked at Tomura in his hands. That is how he knew that the Master's Successor was before him.
The second smell is still a mystery, and one can only wait until Machia is likely to be the one to ask about the second smell and its belonging to someone.
Smell, simply put, is the molecules of various substances that can excite olfactory neurons.
In the vertebrate world, it is common to distinguish between one's relatives and strangers by smell and to strategize about how to interact with them based on that. Most cells in the vertebrate body carry MHC molecules (major histocompatibility complex, in humans called HLA), which act as an inventory of intracellular property. These molecules hold small pieces of cellular proteins like clothespins. Almost all of the cells in the organism exhibit MHC molecules associated with proteins (extra- or intracellular), and these molecules are unique to each organism. It is they that become a kind of protein passport to determine the relatedness of individuals.
In the nose of animals there is the olfactory epithelium, the cells of which carry receptors capable of recognizing a variety of protein sites. It is known for a fact that the receptors distinguish between fragments of proteins that have been linked to the animal's own and to foreign MHC molecules. Close relatives have the same sets of proteins with small inclusions so they will smell very similar, almost identical).
And since Machia has a “dog” quirk with which he can recognize different smells over long distances, probably paying attention to the “protein passport” thesis, he smelled exactly his Master's close relative, mistaking it for the same (second) smell, only weaker and smaller.
Do you think we still have two smells: the Master and the Little Master? Or is it really the smell of Afo in Tomura?
What may well be, without pulling the last strings for DFO: In fact, Machia first smelled Tomura as the new Master (though Machia refers to him as the Crown Master), but was able to smell Afo inside Tomura on the way to Jaku when Afo took control of Tomura's body before burning Endeavor’s fire. But personally, I don't think the second smell came from anywhere. Only if it was an amplification of the influence of the AFO-factor, which somehow changed the body biology, as if it were 2 in 1.
