When you start, Mina is there to congratulate you on Maximum Attack G, (the special event mission, which featured in-game prizes, a live leaderboard on Sega’s site, as well as group prizes. Both kill-count and time-attack could be preformed by teams/individuals to make the photo-enhanced leaderboards. It also had a bit of a plot, accessible here)
Mina assures that the MaxAttack data is enough to please Tomrain and Laia, but still no one really knows what it’s all about and it may be a while before they do. Mina then goes to check the missions available for you, but before she can, she spies someone coming in the door to Guardians HQ. It’s Curtz and he’s staggering in. Leo and Tonnio are in pursuit, yelling ‘look out!’ Curtz himself says “Gi….Gi”

Fight Curtz?
Talk it over?

Talk it Over- Before anyone can speak, he collapses and says ‘gi’. (hence you could not fight him) Leo doesn’t know what’s going on, but comments that he’s finally stopped moving. Mina thought everyone was done for, so Leo explains that they were testing a new anti-seed method on the CASTS when Curtz ran off. He escaped his restraints when Tonnio looked away for a second. Leo says he was trouble before too, and that they’ve got to bring him back to lab 3. You can go too, because there’s no client with a quest waiting.

Maya says that Curtz is fine for now, so Leo and Tonnio agree that he’s not ordinary. They apologize for the trouble, but Leo thinks its odd that SEED influence could be wiped out by a vaccine, and Tonnio agrees. Then, they start grilling Maya as to why only the AMF is still affected…but Lou will explain! As Lou, Clamp Manyel, and Laia have just appeared. Everyone wonders if this is the Host Lou, but it’s not. This is actually the first 'fresh' Lou after all the rest were destroyed in previous chapters. It turns out she was found by Laia on Parum and then fixed. The Host Lou has analyzed the AMF behavior programming and has found a special program with the codename “Brain”. It allows normally autonomous casts to function as a single unit. Naturally, Tonnio wonders why anyone would want to do that, so the Lou explains that it’s the ultimate military tool: "The perfectly cohesive unit”. But, it requires the override of each soldier’s free will. It would generally require ethics to weigh in…so it’s just top secret.

What this means is, it basically creates a hive-mind among whatever battalion of AMF people is required. It stops the androids from controlling their own actions for the period of time the program is run, in order to make the perfect group.

Because the AMF chose to keep that little bit a secret, no one really understands quite how it works yet. But, apparently Illuminus infiltrated it and are controlling the soldiers with the A-Photon waves. It is also strongly suspected that it was what they used to make the AMF attack (and crash) the colony. The next question is naturally about Aphoton waves. What about these?

They’re part of a control signal that’s emitted by “The Brain” to the AMF, but it’s magnified by more a-photons. Maya’s research has been to block it, but so far, it only works if she applies a coating directly onto a bio-chip in an affected CAST. It’s determined that you’d have to do it for EVERY soldier, which is then deemed “unfeasible”.

“So how do we stop it?”

The ideal solution would be to jam the A-waves in the whole system, but that’s hard, due to the still-disheveled state of the Guardians. So that’s why it’s up to you to infiltrate the control facility! No one can re-awaken Curtz until the signal is stopped. Lou requests that Maya be included due to her expertise, and notes that Hyuga has actually been detected there as well! So Maya promptly agrees and Laia says that the AMF is the ‘missing piece’. Leo and Tonnio are also set to go with you.

Roger That?
What About Lumia?

Roger That (The choice likely to keep Lumia away) Everyone is counting on the team. Tonnio, Leo and Lou leave the scene. Maya is upset still about Hyuga, and she’s got a vaccine to completely suppress the virus, but it seems Hyuga is worse. If he’s found, can she even help? So with a bit of a pep-talk from Laia, everyone’s ready to go.

You’re in it with Lou and Maya. Maya immideatly makes a call in to Leo who has Lumia with him. She explains how you’ll be separated this time, and that you’re looking for Aphoton wave transmitters. Maya says she feels something odd in the air, “Rough & consuming”. Lou explains that it’s likely a side-effect of the A-photon waves due to them being at 30 times normal in this area. Curiously Maya then wonders if they have no effect on PEOPLE. (She is a newman, is she considering that newmen aren’t people? The phrasing there is rather odd) She then elaborates that the Divine Maiden can sense the holy spirit in regular photons—so can any newman sense the a-waves? Maya realizes she’s the only newman in the party (IF you are not a newman!) and asks you what you feel. As a CAST, not much so the Lou elaborates that she can sense them but it’s easy enough to just shut them out, but warns that as the team approaches the source, they’ll get stronger.

In this block Vobis, Heavy Infantry and SEED-Argine will try to stop your progress while you listen to Maya to get directions. (she feels worse the closer she gets) Eventually, Hyuga will come staggering in to where you are. Maya wants to rush to help, but Lou wants to do a scan first. Maya asks if it’s Huga:

Without a Doubt?
We Should Be Careful

We Should Be Careful- Maya agrees to be careful, but "we can’t leave him this way". If its 99.999% sure to be him…Someone says No! it’s 100% sure to be Hyuga, and it’s a guy with a guard. Is it Magashi?? Maya yells at the apparent sight of this villain.
Lou, however, sees that it’s not a CAST at all. The guy is now mad, and says “Don’t put me in the category of Magashi and CASTS, as it’s an insult”. Lou explains that you’re now looking at Karl F. Howzer (the human supremacist, hence his remark) who is the aide to the Illuminus leader Rudolf Luntz. ALL Magashis were made in his image. (indeed they look similar, except in skin color and eye-type—Though Howzer even has a scar across his nose mirroring the split in male CAST’s plastic skin) Howzer isn’t interested in the fine details though, and goes to address your band of fighters with Maya as the brains, Lou and then you as the Guardian Ace. He wants to welcome you with the news that Luntz is now dead…because he killed him! (You only see Luntz in the SonicTeam flash animation “Between Games” plot—he was an elderly human general)

Lou can’t confirm if Howzer is telling the truth or not, so he shouts that it all doesn’t matter because you’re all going to die. Maya tells him he can’t get away with it, which provokes him into elaborating a bit. He “Hoped that all branches (meaning defenses) would fall with petty in-fighting (that he was behind) but that ‘you are always in the way’”

Get Over Yourself!
Your Plan Ends Here!

Get Over Yourself! – He knows the comment sounds like something Ethan or Laia would say (but really, either comment sounds like something they might say) and says they’re a thorn-in-the-side too…but that it’ll end here. He then tells Hyuga (who is still quite unwell, but just standing around) that it’s his turn. This causes him to turn into the SEED Venas again, while Howzer makes his convenient getaway.

Fortunately, this time the monster is actually hit-able, so a fight ensues. If you can beat it down, Hyuga falls out of it onto the floor. It doesn’t look good, but he’s still breathing. It seems that the Venas actually forms AROUND the person rather than changing the person INTO the monster such as in all the other cases. In all other cases the person IS literally the monster so by killing it you kill them. With Hyuga though, it seems more like you’re knocking off the monstrous ‘coating’ that he produces. With that drama temporarily ended, Lou goes to shut off the offending computer.

What About Howzer?
Can You Save Hyuga?

What About Howzer? – Maya can’t leave Hyuga but says you can’t go after Howzer alone. (Hyuga is irrelevant at this point, either he can be saved...or he cannot. Howzer however, is in a state of uncertainty) So, call Leo! Maya gives her vaccine to Hyuga and Lumia is glad. The Lou returns after having shut down the PC, but it’ll take time for the effect of the waves to wear off. Maya & you then bring Hyuga back to the Guardians HQ while leaving the rest to Leo.

The AMF-Base Gate.
This is used for equipment and personnel. You start at Laias' area, and it looks like everyone should recover fully. So then why is Laia not happy? The Assistant, Clamp Manyel, fills in that the A-waves have started again. All Lou accomplished was to shut down one terminal, and soon after it went off (Brain Program) the waves restarted from somewhere else. It wasn’t JUST Brain. Whatever’s doing it now is somewhere on the sea floor. This location was always kept a secret from everyone except within the AMF. It’s apparent that Illuminus played everyone. (They played off of AMF’s need for secrecy) A Lou arrives and says that the previous investigation was lacking, and so sorry. There are limited options to hit Mother Brain on the sea floor. Only a small team would work. Maya is watching over Hyuga, and Laya can’t let the Lou go. Everyone else is after Howzer so it’s short-handed....until Curtz walks in!

Everyone is startled, but it’s revealed that his chip has been coated, as he’s a test-case. He woke up during the procedure, but he’s fine now. It’s a difficult procedure, and Maya apologizes that everyone became frightened. Curtz is sorry about everything, so he volunteers himself and…Lumia to go on the mission.

Curtz has been to the facility, so he’ll act as the guide. However, he never knew about Mother Brain being down there. (So who in the AMF is in charge and DID know?) Curtz reveals that he wanted Lumia on the team no matter what (but why?) He then confesses that it’s his first time on a mission with human partners and also that one of them’s a child, so Lumia promptly yells at him. He then states that he feels Lumia could offer something to the mission, (but not what she could offer) so let’s go!

Lumia says the place is different than she expected. Curtz finds it different too, but because of the SEED influence. Lumia had expected it to be more mechanical looking like the AMF building. This prompts Curtz to realize that he doesn’t remember anything at all from his time of being out of control.

It Was Tough!
Don’t Worry About It

Don’t Worry About It – He’s glad to hear it. The 'toughness' could be interperated either way, either he was 'tough' to corrall while OOC, or as that it was 'tough' on him The response option is vague and not as relevant. He will free all of the AMF as his apology to them for failing as their leader. (Curtz’s actual rank is not quite clear. He’s a squadron leader, later promoted to head of the Anti-SEED task force, but this is only equivalent of a General, and not an Admiral/High-General who would be in charge of the entire AMF—his statement here only further muddies it) Lumia assures him that it’s not his fault and that Illuminus exposed a fault in the AMF plan. No one deserves to have their free will removed and ignored. Curtz views the mission as atonement for fallen comrades used as Illuminus puppets. He calls Lumia “Dear” which surprises her. He asks if it’s incorrect to use the term on young human females. She says to just call her “Lumia”. This is actually a little on the creepy side and may cause feminists to bristle a bit. However, it’s a curious character interaction.

You get moving again, and need to fight AMF Heavy Infantry, Orcdillans, traps and various monsters to get to the next area on a time limit. In the next area, Lumia has a problem. Curtz tries to guess at it with “is she tired”? Are all Guardians this way? (As in, assuming that flesh-based creatures are quite easy to wear out) Lumia then accuses him of being ‘such a cast’. But is it because he willingly offs his comrades without emotion? (Remember AMFHeavy Inf. (but NOT Vobis because Vobis was always alligned with Illuminus, even saying "Forgive Me, Howzer!" when killed) are actual people who COULD be saved if they could be stopped, and have their chip coated. Here, they're just being mowed down in order to progress)

It’s Part of Our Mission
It’s Likely Tough For Curtz Too

It’s Likely Tough For Curtz Too – The Guardians offer to help anyone in need. Lumia though, feels she’s not helping. (that is her problem) Curtz recognizes that he doesn’t emote well, but he understand the concept of painful thoughts and experiences. This brings up the recollection of Laia vs the runaway beast in the caves who turned into a monster when he couldn’t receive the vaccine. (See other mission) Lumia puts it all together and is surprised that CASTS can have emotions.
This causes Curtz to make a speech: Curtz explains that they do, but since emotions are not logical, it’s put on secondary processors. Emotional reactions/over-reactions can be fatal on missions. (IE this makes it easy to abandon comrades to achieve the goal anyway) During his period of cast supremacist belief, he looked down on all others who had emotions. But, as he fought on he started to understand people and what he was fighting for. (It can be logically assumed that it is somewhat in part due to Ethan's actions in Offline Story Mode PSU. Curtz even mentioned something to the effect.).

Lumia then changes her mind and says he doesn’t sound CAST-ish. The idea of cast-like or non-cast-like is also wrong. Everyone is an individual, with faults and strengths. However, now is not the time to worry about it. It’s what will unite all races to finally beat the Illuminus and SEED. Everyone agrees, so it gives Curtz hope. Curtz acknowledges that Lumia is a good person, and that Mother Brain is ahead, though he doesn’t know what it’ll be like. He has no concept of having a Mother, but is sure that this is one that no one wants!

Curtz wonders if he can make up for everything that’s gone on. What the AMF did and also went through. Lumia, in a stroke of brilliance says that “That’s up to what he does from now on!” It’s actually quite a wise statement. But what will the AMF do now? He has ideas but wants to restructure and re-examine. There’s only 1 thing in the way of peace now (but what? Seed, presumably) He then thanks everyone and needs to put an end to this place. He’ll do that, and then meet his fellow soldiers freed from the curse of the A-photon waves. He’ll contact everyone later, and says to give his regards to Laia.

So everyone goes home, and Curtz and the AMF promise to restore a real alliance that pledges to assist all Guardians until the seed menace is gone. Laia, interestingly cheerful, says Let’s go get ‘em! They shake on it, and all the soldiers are restored. And now, that the AMF are also allied, the real struggle is still yet to come. You then obtain Curtz’s Partner Card.

End note:
This chapter is also a nice and tidy one.
Hyuga is now permenently fixed, and the Venas menace/mystery is no more
The final group (AMF) has now been brought in line with the rest to help crush the SEED
No more rampaging CASTs, with the Aphotons shut off
Maya's vaccine now must be top-notch-fix-anything if it could cure Hyuga so no more people-into-seed shennanigans need take place
Howzer got away, but Leo is on the case
The Lous are doing better

Again, it didn't raise any questions that it did not answer. It actually also fixed several previous problems, venas, AMF rampage, an AMF secret.