There are a few things to consider in this.
For starters:
The Satellites confirmed the agents were seen off safely, yet not only were they were attacked by the Sea Beasts but brought back all the way to Labo's basement and nobody noticed.
The shadow is exceptionally elusive, no camera caught them and Shaka made a comment how cams may have been knocked out of position.
I have seen people say, serious and not about Shiryuu?
There would be no need to take out cameras. This is someone who doesn't want to be seen by the feed.
Communications are down and further establish someone seems to know their way with Egghead technology. They are keeping everyone dark. No cams nor comms and even cutting off security at Labo was no problem it seems.
Along with the agents brought back with nobody noticing, this shadow is seen by noone either. Pythagoras may have had an encounter but even so, this phantom seems to know the layout of Labo in avoiding everyone. Putting everyone in the basement may add into that too in knowing the place well.
Let us go by process by elimination.
York is stoned. Lilith is stoned. Edison got wrecked. Pythagoras got trashed. Shaka got shot.
Atlas is twice the odd one out now.
The only one who was at Labo when security went down and seemingly her group not being engaged in a fight.
Doesn't necessarily mean it is her.
Lilith was unaccounted for when the shadow appeared and Pythagoras was wrecked. And the latter was patrolling alone. Nobody had any free movements otherwise cause they were always shown with multiple people, including Strawhats.
York is missing now as Shaka was shot.
Just to get those statuses out.
I was contemplating if the Satellites are all in on it, doing switcharoos of who does what or when and are gaslighting Stella and the Strawhats but I wouldn't know why.
Regarding the traitor, I noticed something in this chapter that is not leaving my brain. I dare not want to call it an analysis – but rather a very fragile theory, which is standing on wobbly legs. Please do not treat it as something with a strong foundation – it is lacking much if it. Bad enough that I am writing it down here… .:
We all know that the Satellites have different purposes. And in the beginning, we see those very clearly described when every one of them is introduced.
Take a closer look at Pythagoras: His main task is analyzing the projects, which are being tested. Projects like the Seraphim. Here we see him going over the data and noting changes and coming up with different ways to improve them (chapter 1065). He is also the one, who always has a constant eye on the monitors. Even if Shaka is right next to him, it is Pythagoras, who is observing everything and conveying that information to Shaka. Seeing him doing that for the last few chapters, reminded me that his position as someone who monitors the whole of Egghead, is a very critical one: In case something happens, Pythagoras would be the first one to notice. And he would be the first one the other Satellites would ask, if they wanted to make him convey what he saw on the monitors or from the data.
And in any case that there was someone who was dragging back marine ships with CP agents aboard, Pythagoras should be also the one, who notices it first, right? (By the way: Did you notice that the agents asked Shaka, if was he the culprit? That means those agents have not been dragged back by the traitor him-/herself, but by beings the traitor used to do the job. Maybe those Pacifista or a Seraphim. That means the traitor has some authority over them.). He told Shaka that no one was in the control room, when the Dome shut down. He was also the one, who was able to bring up the dome again.
The thing is: Pythagoras could lie to his collegues faces and they would believe him to the bitter end, without even realizing that there was actually someone in the control room, or that Pathagoras had brought up the Dome again by himself. And maybe he only told everyone that he has seen those WG-ships depart from Egghead safely.
Now in chapter 1074 we see him looking for the Stellar and obviously being blown up. But looking a few chapters ahead, we see only his body being damaged. His head is still intact. I wouldn’t even call that thing his body – I would rather consider it a tool he uses to move. His real body seems to be only the round sphere he calls his “head”.
So, all in all the damage he was receiving with the blow is not really affecting anything important, seeing as his “body” can be repared or even exchanged with the technology they have at hand. It was totally expandable.
In the last chapter 1077 now we see the group of Franky, Usopp, York and Lilith being attacked by S-Snake. All were seeing being turned to stone – everyone except for Pythagoras.
Where is he?
By the way – we could not see if the Seraphim were actually following his command, because he was never seen trying to give any orders to them. Therefore, we still don’t know if they would follow his orders.
He is also lacking character and seems rather bland to me – like Oda is not putting in much effort for him. Granted, he is a robot, but then – Edison is a robot, too. But he comes off as someone with a much more emotional colorful character.
On another sidenote – Pythagoras was also the one, who was suggesting to call Stussy – who I am also not thinking of being on Vegapunks side at the moment.
Also, if I were a Satelite and the traitor, I would try to secretly reprogram the important tech that I know will be useful in the future. And I do not only mean the Seraphim (The command chain could be, for example, being modified) – think of the Dome or certain other stuff. And like I said before – the traitor would have had a lot of time in preparing for the day that has now come.
