Sarge, the doppelganger of the late Phil Coulson, isn't Marvel's Agents of SHIELD season 6's real villain. The mystery man with the familiar face arrived on Earth as the leader of a mercenary team from outer space consisting of Snowflake, Jaco, and Pax. Sarge's ruthlessness was immediately established when he killed SHIELD. Agent Fox as soon as he appeared and yet, as dangerous as he is, there is more going on with Clark Gregg's new character than fans have seen so far. Sarge certainly acts villainous and his team has cut a path of destruction; they've already battled the Agents led by the new SHIELD Director Mack Mackenzie, and the very fact that Sarge looks exactly like Phil Coulson has drawn the ire of Melinda May.
In this week's episode of Agents of SHIELD, "Code Yellow", Sarge's group attacked the headquarters of Deke Shaw's virtual reality start-up based on the Framework. At first, Deke was fooled by Sarge's attempt to impersonate Coulson but Deke soon figured out the doppelganger was there to kill him. Sarge isn't a talker like Deke but he drops clues about his true mission when he does speak, like when he told Deke that "you're not from here and you shouldn't be here". Sarge's group has a tracker that knows Deke was supposed to be erased from existence when SHIELD changed the timeline in season 5 and he even said he's been hunting Deke's kind his entire life.
Elsewhere in "Code Yellow", however, a discovery by Dr. Marcus Benson hints at the real threat of Agents of SHIELD season 6 - the one Sarge has actually arrived to fight. At the start of the episode, Sarge's team tracked a man named Harold Simcoe and the fake Coulson stabbed him with a knife in the chest, at which point Simcoe began manifesting spikey protrusions. But when Benson performed an autopsy on Simcoe, he found out there was a parasite inside the man's chest cavity that resembled a black alien bird. The bird suddenly escaped and then infected Agent Keller, transforming him from the inside so that he also began to emit crystal-like spikes and it only stopped when Yo-Yo Rodriguez plunged the same knife that Sarge used on Simcoe into Keller.
It's possible these aliens have infected other people and this is the enemy Sarge's team is really hunting on Earth - meaning SHIELD is inadvertently in their way. Why Sarge's group thinks Deke is a target isn't clear, but Jaco indicated there was something strange about how their scanner was registering Deke; perhaps it was confused by Deke's actual status as a time aberration. Eliminating people who don't belong in the timeline is why the Chronicom Hunters that Daisy Johnson's SHIELD team is facing in outer space are targeting Leo Fitz, as we saw in last week's episode, "Fear and Loathing in the Planet Kitson". However, it's not clear whether Sarge's squad is related to the Chronicom Hunters.
Killing the alien parasites infecting humans could also be why Snowflake is so enamored with her job of "making butterflies". The parasites seem to be turning their hosts into something else entirely, like how a caterpillar is turned into a butterfly. This revelation also changes the footage Mack and Benson saw of Sarge's team on another planet in "Window of Opportunity" - the wave that was destroying the planet may not have been caused by Sarge but instead was what Sarge's squad was trying to fight.
At the end of "Code Yellow", Sarge captured May instead of killing her, so he must need her help. The mystery of why Sarge looks like Coulson still has to be answered and it will be a huge hurdle for May and SHIELD to trust the fake Coulson, but it seems like they have a common enemy in these unnamed alien parasites - Agents of SHIELD season 6's real villains.
Marvel's Agents of S.H.I.E.L.D. airs Fridays @ 8pm on ABC.