History Headscratchers / PerfectDark

** I can agree with you on everything but Johnathan. From the cutscene in Perfect Dark in which you meet him, it seems more like they do know each other, it's just that Joanna was still in "shoot everything that exists" mode, and Johnathan startled her.
** No, in the original game, she comes upon a mook that she clearly ''thinks'' is Johnathan before Johnathan reveals himself.

** I think Joanna knew exactly who Johnathan was and what he looked like. His facial features stayed the same and the dialogue is very indicative of their familiarity. The camera hides him from view until his reveal but it can be assumed he was just out of view because of the guard he had to shoot. The dialogue from Joanna: "There you are. I was beginning to wonder if you'd been discovered yet. (after John has shot the enemy) And frankly, if this is how you work I'm surprised you lasted longer than five minutes."

* If we are to accept everything in both console games as canon, then since joining the Institute, Joanna has adoped an english accent, been labeled "inexperienced" (despite the fact she used to be a bounty hunter and defeated a "god") and forgotten what Jonathan looks like.

*** Well he doesn't ever look comfortable in that suit, does he?

*** No, in the original game, she comes upon a mook that she clearly ''thinks'' is Johnathan before Johnathan reveals himself.
*** Undercover agents can be wearing all kinds of disguises.
*** The game doesn't refer to the undercover agent as Jonathon until the mission briefing in Area 51-Rescue. Joanna just doesn't recognize the voice, which has changed just like Joanna's voice has.
*** I think Joanna knew exactly who Johnathan was and what he looked like. His facial features stayed the same and the dialogue is very indicative of their familiarity. The camera hides him from view until his reveal but it can be assumed he was just out of view because of the guard he had to shoot. The dialogue from Joanna: "There you are. I was beginning to wonder if you'd been discovered yet. (after John has shot the enemy) And frankly, if this is how you work I'm surprised you lasted longer than five minutes."

** Simple: the in-universe discovery of cloaking technology required AppliedPhlebotinum in the form of rare mineral bullets, which also happen to be on par with regular bullets in terms of lethality. Obviously the specifically designed cloaking device uses the mineral but in a shape/form that can't double as ammunition. They can afford the RCP-120 a short residual charge, long enough for a skilled user to do a reload in a short space of time and allow the next magazine/effective battery pack to carry the charge on (at the cost of a fuel deficit which the next few bullets have to automatically burn off to pay for the residual charge). If the user runs out of ammo, the gun can sense that there are no more mags on their person, so it won't be able to permit the residual charge. The weapon designers recognised that unless the user specifies otherwise, they'd probably appreciate being able to stay invisible rather than suddenly (and inconveniently) appear in the middle of a hostile area.

** Simple: the in-universe discovery of cloaking technology required AppliedPhlebotinum in the form of rare mineral bullets, which also happen to be on par with regular bullets in terms of lethality. Obviously the specifically designed cloaking device uses the mineral but in a shape/form that can't double as ammunition. They can afford the RCP-120 a short residual charge, long enough for a skilled user to do a reload in a short space of time and allow the next magazine/effective battery pack to carry the charge on. The designers recognised that unless the user specifies otherwise, they'd probably appreciate being able to stay invisible rather than suddenly (and inconveniently) appear in the middle of a hostile area.