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I think the sky temple key clues were one time scans, because after you put a key in, you cant get the clue. The webtrap that appears during the ing warrior fight is also a one time scan as far as I know, and of course there are the bosses. I guess ingsmashers are one timers too.....or maybe like six timers...I forgot how many there were.
Thread title: 
you don't automatically get the clue when you return the key?
What luck, there's french fry stuck in my beard.
No--that made me restart...
All the sub bosses and bosses are probably an automatic one time scan. Those clues are a 1 time chance, sort of. What I would do is before you step into the "thingy" (the switch that activates the cut-scene fore the keys) scan the clues. I'm not sure if this helps or not because i have no idea if after you collect a key, the clue goes away. just my thought. :?
As a matter of fact the clues are NOT one time only. I found a key before i knew what it was and placed it before I knew what the temple was, so I missed the clue before I placed the key. Now I finally went back there with all of them and the clue was back for scanning.
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Ready and willing.
I think you just can't get them any more once you put all the keys in.
Quote from Yoshi348:
I think you just can't get them any more once you put all the keys in.

Thats kind of what I was explaining, but it works so everyone is happy  :D  :D
Where are these 'clues'
They're all in the Dark Aether version of the place you get the Seeker Missiles at.
>_>

Sky Temple Gateway, the dark version of Hall of Honored Dead.

Didn't even need to check my map. o_O
I'm learning the room names already, just like how I did with Prime.
I think the only one time scan I missed was the some part of the Chykka Fight, the smaller bugs that it throws at you is my guess.

However, that wouldn't really account for the missing 8%....
shrimp
and white wine
Am I supposed to have scanned the Spider Guardian? Is it even possible to do so? :(
Quote from Soap on a Rope:
Am I supposed to have scanned the Spider Guardian? Is it even possible to do so? :(


Yep, its possible, before you fight him you can see him in the windows in the wall and scan that way.
Hm, i remember, in the beginning of the game, well, if you go back to the beginning of the game... you fight a darkling missile trooper (or something of that sort)

I know that its a one time scan, but i also remember it dropping a different looking missile upgrade, was that thing a one time scan as well?
What luck, there's french fry stuck in my beard.
Nope.  Expansions and items and such aren't log book scans.
red chamber dream
I always thought that they should count as logbook scans. They can be necessary for survival, you know. Plus, they'd be easy scans.
Well, they counted in the first game, but this one has so many Research entries that it probably wasn't needed. *shrugs*

As for one-time (as well as super-rare) scans, I believe this is a complete list, but I probably left off some, in which case feel free to add to it. I'll mark it as a spoiler so as not to disturb those who have not completed the game yet but who are still reading this thread.

Quick edit: Well, wtf, the spoiler tag won't include text included in a list bracket. Oh well.

Creatures:
    Aether -> Aquatic -> Large Aquatic -> Alpha BloggAether -> Ground -> Predators -> Alpha SandiggerAether -> Ground -> Predators -> Alpha SplinterAether -> Mechanoids -> Stationary -> Caretaker Class DroneAether -> Mechanoids -> Stationary -> Vigilance Class TurretDark Aether -> Darklings -> Darkling Aquatic -> Dark Blogg *Dark Aether -> Darklings -> Darkling Flyers -> Dark ShredderDark Aether -> Darklings -> Darkling Mechanoids -> Dark Diligence Drone**Emperor Ing -> Emperor Ing BodyEmperor Ing -> Emperor Ing HeadEmperor Ing -> Emperor Ing EyeEmperor Ing -> Emperor Ing ChrysalisEmperor Ing -> Mutated Emperor IngGuardians -> Amorbis -> Amorbis 1Guardians -> Amorbis -> Amorbis 2Guardians -> Chykka -> Chykka LarvaGuardians -> Chykka -> Chykka AdultGuardians -> Chykka -> ChyklingsGuardians -> Chykka -> Dark ChykkaGuardians -> Quadraxis -> QuadraxisGuardians -> Quadraxis -> Damaged QuadraxisGuardians -> Quadraxis -> Shielded Head ModuleGuardians -> Quadraxis -> Stunned Head ModuleGuardians -> Quadraxis -> Final Head ModuleGuardians -> Sub Guardians -> Bomb GuardianGuardians -> Sub Guardians -> Jump GuardianGuardians -> Sub Guardians -> Boost GuardianGuardians -> Sub Guardians -> Grapple GuardianGuardians -> Sub Guardians -> Spider GuardianGuardians -> Sub Guardians -> Power Bomb GuardianIng -> Ing Larva Swarm *Offworld -> Dark Samus -> Dark Samus 1Offworld -> Dark Samus -> Dark Samus 2Offworld -> Dark Samus -> Dark Samus 3Offworld -> Dark Samus -> Dark Samus 4


Lore:
    Luminoth Lore >> A-Kul's Clues >> Cadre 1 Clues >> B-Stl's KeyLuminoth Lore >> A-Kul's Clues >> Cadre 1 Clues >> G-Sch's KeyLuminoth Lore >> A-Kul's Clues >> Cadre 1 Clues >> J-Stl's KeyLuminoth Lore >> A-Kul's Clues >> Cadre 1 Clues >> S-Dly's KeyLuminoth Lore >> A-Kul's Clues >> Cadre 2 Clues >> C-Rch's KeyLuminoth Lore >> A-Kul's Clues >> Cadre 2 Clues >> D-Isl's KeyLuminoth Lore >> A-Kul's Clues >> Cadre 2 Clues >> J-Fme's KeyLuminoth Lore >> A-Kul's Clues >> Cadre 2 Clues >> M-Dhe's KeyLuminoth Lore >> A-Kul's Clues >> Cadre 2 Clues >> S-Jrs's Key(I went back and tried to scan the ones I hadn't in my first file, and they wouldn't register, so...)


Research:
    Biology -> Darklings -> Ing Webtrap +


* not sure about these, but I've only ever seen one or two, in only one room.
** these appear in only one area, but can be re-scanned.
+ MUST be scanned before you defeat all the Warrior Ing (the room where 5 of them attack).

Again, if I missed anything or added something that wasn't, let me know :P

-Tim

edits: accounted for the Grenadier and GF Bridge entries as non-one-timers, thanks.
Also removed Dark Quad CM as well.
Heh, now say bye-bye to Dark War Wasp, Blueroot Tree, and Lightbringer ;p
What luck, there's french fry stuck in my beard.
You can still scan the GF bridge after you lower it, but yeah, there's only one.
red chamber dream
I know that Missile Expansions and Energy Tanks counted in Prime I, but items such as the Wave Beam did not, correct? They ought to, though.
Pirate Grenadier is always available once you pass some specific point that I can't remember. There'll always be two in that pirate room with the... bah. You know in the demo, that room where you go to the dark world? In there. There's always two grenadiers there after some point in time.
Actually, I get the Dark Quad CM scan without disabling the legs.
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Ready and willing.
Quote from Xin:
Actually, I get the Dark Quad CM scan without disabling the legs.


I can confirm that.
Quote from Tim:
Dark Aether -> Darklings -> Darkling Flyers -> Dark War Wasp **

I've come across the Dark War Wasp in two rooms, the Vault Attack Portal (Dark World, where the Screw Attack is.)  The other room is the Service Access in the Light World Temple Grounds, after you get the Light Suit.
red chamber dream
When you revisit the rooms though, are they still there, or are they like the Ice Shriekbats in Prime I and disappear?
What the hell is Amorbis 2?