Scenario 1 Part 2
After restocking much needed supplies, and saving your progress with the guild lady, Natasha clears you for access to ragol through the teleporter. Elly says you don't need to accompany her, you've already done what you were paid to do. But if you didn't, what would be the point?
Once you reach the CCA and see a cut-scene over-view, Calus contacts her again. His message comes to the both of you over the navigation system, and is rather broken up. He mentions getting to the end of CCA. After fighting some rooms of enemies, you learn that Calus wants to take on a human form so that he can be with Elly forever. He knows the means to do it are possibly contained within the Control Tower. This was where the presumed Dr. Calus created the CALS system before he died. He also created a mysterious device known as MOTHER which could be the key to Calus' becoming human.
However, the CALS-System does not want this rogue part of itself endangering the whole system, and re-appears to stop him when Elly accesses another computer terminal in order to set the proper coordinates to the Control Tower. During the confrontation, the System says that Callus' actual chance of succeeding in his quest is 0. (It has run the situation through a simulation) It also doesn't want him to change the evolutionary path of the AI entity that makes up the system, and will kill him if he has to, to stop the plan. The System insists that Callus is dead, and that he died when Vol-Opt or the D-cell infection affected the original when he was installed down in No Mans Mines.
The System claims that it cannot lie, and that lying has no meaning anyway. However, Callus proves this wrong, by admitting to a lie just a moment later. As it turns out, he really did die down in the mines and that what you see now is just a copy. However...it doesn't matter. Being a machine, the back-up is identical in both memories and feelings to the original. With power in the navigation system running low, they both transform back into the balls of light, and vanish, but not before the System locks down the final gate to the Control Tower teleporter.
You now have to figure out a way to get it unlocked. For some reason, you also have to scold Elly when she seems indecisive, although yelling at her in a time like that would seem highly un-productive. There happens to be an emergency access panel below the path you are on now, which forces you to jump the railing, and fall down the steep incline to reach the area below. (thinking about it doesn't help) After worrying Elly and fighting a Gibbles as well as some Sinows, you can unlock the final gate.
The Central control area is filled with computer panels, each with a single spike of energy running through them. They are the security system to the building, and it relies on decoy terminals, instead of difficult codes to thwart unwanted guests. On each floor you must choose the correct terminal, or it will warp in a difficult to defeat enemy. However, you also have the option of shooting any of the terminals, which also sets off the security system. Unfortunately, the facility also contains numerous Recoboxes positioned right next to terminals. Elly usually won't follow you, or access a panel until after the Recon threat has been neutralized. This makes it very easy to accidentally target a panel, and set off the system. In most cases, the living cannot cast any RA or GI techs without tripping more then one wrong panel, making everything especially difficult. The various things that can be transported in for a fight include: Gibbles, Mericarol, Gi Gue and a new enemy, the Del Lilly. All of which generally have the ability to kill Elly in one hit.
If you reach the end of the Control Tower, there is an all new room which contains a strange and beautiful blue vortex in both the floor and the ceiling. The "vortex of life" was created by Calus' Father to create the next form of life. It is never explained what this form might be. However, Calus knows that the vortex also has a chance of creating for him a human body. The System Collective does not want to stop evolving as an AI, and it finally agrees to cut off Callus so that he may do as he wishes. The System claims that to become human would cause evolution without potential. Callus says he knew the journey to watch him come and choose, as well as the choice itself was painful for Elly to do, but it was what he wanted most. He was not even sure he wanted to go through with the risky procedure, but whatever happened, he knew he wanted her by his side. Callus steps into the vortex and vanishes, promising he will return for Elly if he can, and that he will be with her forever.
Afterward, you are dumped on the beach of Gal Da Val at night, unconsciously teleported there. If you walk around, the whole level is empty, except for a warp, which leads to a cliff top, and Elly. Elly is still sad over what happened, and wonders if she will see Calus again. If you follow her, she explains why she wanted to join Pioneer 2. It was to be a real hero, like Red Ring Rico, who she so admired. As Rico dissappeared, the world looks for another hero. She speculates the next one could even be you. She does not think she is very heroic at all, but who else could have risked so much, and put so much of her care toward a fascinating and kind machine. She worked so hard to save Calus, without ever questioning it, and helped him believe in what he could do. Elly ended up a hero after all.
Talking to the NPCs on P2, it is revealed that the CALS system was able to be fully recovered and functional once Elly returned to the ship. However, he still has no body.