So, Bowman’s story in Episode 57 is really fishy. And that’s without us as the audience knowing the massive red flag that is the fact that Bowman’s memories have probably been rewritten tens of times in order to achieve whatever goals are assigned to him. This could easily be yet another fake set of memories. After all, this story is obviously going to throw Playmaker off focus, and if the end goal is to take over his body, then of course you’re going to take every advantage you can get.
Having someone inside “Yusaku Fujiki’s” body, but with completely different allegiances and motivations. This would be the perfect “spy”, and as we know, Yusaku has absolutely no contact with anybody right now, outside of Ai. However, if he loses and gets his body taken, they can easily just take Ai and have “Yusaku” claim that he lost and that Ai got taken. There would be nobody to disprove him.
I can see them making a backup of everything that Yusaku is. This probably would have been needed in order to assist in creating the Ignis. But there shouldn’t have been a need to create an entire backup “person”, with their own thoughts and feelings, just digital, let alone a way for the backup to be switched with the “real” person. All of the data could have been stored separately. Even more, from what we see it looks like the consciousnesses were switched almost instantaneously, too. It doesn’t seem logical for what would only need to be a pure download of Yusaku’s “everything” (I guess we can call it that) to suddenly open up an opposite connection and instantly switch the copies. (I’m not going to say that there isn’t wiggle room here, because we didn’t really know much about how the hanoi project actually worked until now, and even then it might just be a massive lie to mess with Yusaku)
Another point is that Bowman doesn’t seem to know Yusaku’s name. He doesn’t mention it a single time in the episode (from what I remember), and while it could be waved off as him thinking of himself as “Yusaku”, there’s also the possibility that they don’t actually know it. If they knew his name, they could have thrown it out at him, for example, rather than Bowman claiming “I am you, and you are me!”, he could have yelled “I am Yusaku Fujiki!”, or something similar. This probably would have thrown Yusaku off, a lot more than what Bowman had actually said in the episode. Playmaker even directly asks “Bowman, who are you?”, and Bowman’s response is “I’m a victim of the Lost Incident ten years ago.”. It seems like he’s avoiding actually stating a name. If he believes he is the real Yusaku, why does he not say that’s his name?
Next, he claims that, because he’s the “real Yusaku”, he knows everything about how Playmaker duels. This, just, no. We’re talking about a 10 year gap here. It’s very unlikely that Yusaku duels the same way as he did back during the hanoi project, especially considering that, as far as we know, the cyberse cards didn’t even exist back then. There is plenty of footage of Playmaker dueling, so it wouldn’t have been too hard to analyse his play style and figure out some logical counters to it.
Finally, we can get around to addressing the major red flag about Bowman’s memories themselves. We know that they can, and have, been rewritten. His boss, at the start of the episode, says “Wake up, Bowman. Along with your new memories. Playmaker is coming.”. Obviously, some kind of memories have been implanted into his head. And, right before the ending plays, Bowman talks about how he’s been waiting for this day to reclaim his body. The view pans to Haru. He’s smiling, and gives a short laugh. Almost as if something is going all according to plan. Given that Haru seems to be in on the whole “manipulate Bowman’s memories to our own ends” thing, it probably is. If the aim of implanting these memories into Bowman’s head was so that he would use them to cause Playmaker to lose focus, and then win the duel, then it’s worked. Playmaker has just been told that he’s not the real him, so he’s well and truly thrown for a loop right now.