I know I'm late to the party but I just finished the game last night...and wow. that was pretty epic, mindblowns everywhere. Is just as good as 999 which is quite the feat I would say.

I making this thread mainly because I still have some question:

1) It's clear that old Sigma and Phi failed in the mars project and Radical-6 got out, that's when Sigma lost his arms and his right eye. But the question remains, the "young" Sigma at the beginning of the game had the mechanical arms? I mean the Sigma ending shows that he indeed had mechanical arms, but I still don't get it. When old Sigma lost his arms did it change the future, or did he lose the arms from the very beginning (before he even began the research and plan the Nonary game)? Did old Sigma (Zero Sr.) had mechanical arms while planning the Nonary game?

2) Why did Akane made Clover sleep for 45 years? I get why she was there but why bring the young Clover, wouldn't it made more sense to do the same thing as Tenmyouji (Junpei) and bring an older Clover? After all she lost 45 years of her life and her brother (Snake) is probably dead.

3) There's going to be sequel right? According to Wiki there's a sequel in development but has there been any more news about it? I want to know how this ends dammit!

The game was really amazing, and in some aspects is better than 999. There are only a couple of things I didn't liked, but those are nitpicking stuff. Overall amazing story and one of the best I've experienced since 999.

A great game, no doubt, but the way the plot was written/paced is quite controversial. Some things you just can take with your own interpretations. I personally think that:

1 ) The Sigma that played the 3rd nonary game was all the time the older Sigma, but with the conscience of the younger one (the young Sigma "jumped" to the future), despite what one of the endings show.

2 ) I don´t have a clue, but I believe she wanted Clover to be there because her hability to use the morphogenetic fields could be useful for the project

3) The plot directly points to a sequel, but there´s no word from the developer about it yet. I´m afraid with the future of the series, since it seems that this game didn´t sell well.

I recently finished the game, too. Excellent story.

1. Remember, the story deals with the future affecting the past. I don't understand it completely, but I think it's got has something to do with it. It would explain why Sigma didn't know about the mechanical arms even though they've seemingly been there for a long time.
2. That's never fully explained, ut I believe that it's possible something might've happened to Clover in the future that made getting an older version of her impossible. Therefore when they had the chance to grab her with Alice they just found that to be more convenient.
3. If you get the secret ending, obtained by getting all of the gold files, it absolutely screams 'sequel time.' And since they never fully explained what happened at the facility to cause Radical-6 (or what necessitated the mechanical arms), I'd say a third game is inevitable. Not to mention that we really learned barely anything about Phi, when you think about it.

The young Sigma who is kidnapped at the beginning of the game has his consciousness bumped forward to the future. The old Sigma who takes over his body loses the arms a few days after that, so the first Sigma never knew about the mechanical arms. They were there the whole time, though.

VGC didn't tracked the game, but apparently 999 sold 28k units which I guess was ok for the production values of the game, and they made a sequel which I guess meant the game was somewhat successful. I imagine Virtue's Last Reward did around the same numbers, but the production values were higher this time (3D animations, voice acting, etc), so maybe they didn't made the cut this time around. 

1) I understand why he thought he didn't had the mechanical arms, my main question is when Sigma lost his arms in the first place. Did Sigma had mechanical arms before the nonary game? or did he lost them when the first jump was made? 

3) Yeah I got the secret ending, and it obviously points to a sequel, and according to Wiki it will be the end of the trilogy. I just hope it doesn't take to long to come out!

So "old" Sigma's actions in the past did change the future? Then "young" Sigma always had the mechanical arms.

But that means, at the very beginning of everything (when Sigma was doing his research and planning the nonary game) he had his arms correct? 

I sincerely hope that they produce the sequel. It´s meant to be the third and final chapter of the whole story and I´m really curious about how it would end. Presumibly, it won´t be a nonary game again, but something different, since Sigma and Phi will team up to avoid the loss of the virus

I don't have space on my memory card to put it on

By "his" arms do you mean his original arms or the mechanical ones?

He loses his arms and right eye during his stay on the Nevada Test Site when trying to avoid Radical-6 to be released on the air.

That happens after the kidnapping and before his trip to the moon,  so the young Sigma wouldn´t be aware of his mechanical arms, since those memories belong to the older Sigma.

Now Akane wants him to go to the Test Site again to try to avoid it. As the plot says, it will be his second time on that place, the virus spread because he and Phi failed their first attempt

Kind of confusing, isn´t it ?