Items Collected:[edit]
Weapons:
Chain Rod
Shield Boomerang
A New Leader[edit]
The game will shift to a cutscene of the New Resistance Base, a far superior and much nicer base, compared to the old, decrepit one of the first game. A group of Resistance Soldiers, with a pair of lieutenants, Isosu and Pasosu, are listening to the welcoming speech of a Reploid named Elpizo, who has been appointed as the new commander of the Resistance. Elpizo is pleased with his new position as leader, and the completion of the new base. His speech causes his soldiers to cheer him on as they file out.
Afterward, Ciel walks into the room to find Elpizo wondering if it was a good idea to make him leader. Ciel stepped down to spend more time on her research on the energy crisis, and after Elpizo's extrodinary actions he took to organize and strengthen the Resistance, she's very confident in his abilities. However, Ciel warns him that they organized the Resistance to defend themselves, not to go to war. Elpizo tells her he's buying time for her research before Copy X is eventually rebuilt. Ciel tries to make him promise not to be too strict as a leader, but Elpizo doesn't gets the chance to respond. Their conversation is interrupted.
Colbor rushes into the room and informs both of them that they've just found Zero lying unconscious outside the base. Immediately, Ciel springs into action with several soldiers to rescue him. All Elpizo can do is watch...
Maintenance Room[edit]
Now, the cutscene shifts to the maintenance room, where Zero is recovering on a repair bed while Cerveau monitors his condition. Finally, after lengthy repairs, Zero wakes up, much to Ciel's pleasure. Cerveau raises the repair unit so Zero can sit up. Ciel's immediately expresses her relief that he's okay, and fills him in on what has happened since his long absence, along with an apology for not getting the chance to rescue him. Meanwhile, Cerveau is also happy to see Zero alive and well, and fixed his weapons. Cerveau even has a new weapon to give him. Ciel and Cerveau both want Zero to pay a visit to them, and leave the room.
Exploring the Base[edit]
Now that you're in tip-top shape again, check out your subscreen. It's been upgraded to a new, cooler-looking version of the first. There are also a few other subscreens that have returned, such as for Cyber-Elves and EX Skills, a new feature that will come into play later. For right now, you should pay a visit to Ciel and Cerveau. Leave the maintenance room, and you'll run into Colbor. He mentions that new Resistance soldiers have arrived, and have yet to meet you. You can meet a new member by going back inside the maintenance room. Rocinolle, the Resistance medic, will talk to you. However, you need to visit Ciel and Cerveau first, and you can't go past Colbor, so head down the hall to the right and enter the door marked CMD. You'll enter the command center.
Zero will meet Elpizo for the first time. Elpizo explains his part in things, and wants Zero's support to destroy Neo Arcadia. Zero has disbelief in his plans, because doing so will be extremely difficult, but Elpizo doesn't see any other solution to their problems. He gets a laugh out of Zero's confusion and calls him Mr. Legend, but gets the feeling Zero doesn't like him too much.
Visiting Cerveau[edit]
Head further to the right after your chat with Elpizo to find two doors marked LAB and CIEL. Since Cerveau has his own lab now, it's time to see what work he's accomplished with the proper equipment. Go inside and speak to him.
Cerveau greets Zero, but expresses dismay that Zero used his weapons so much that they wore down and broke. Fortunately, since Cerveau invented them himself, he fixed them up, and then some. He'll give you his newest creation, the 
Chain Rod, an upgraded Triple Rod, and also hand back your 
Shield Boomerang you had in the last game. Like the other weapons, you'll need time to level them up again. The one you might have trouble adjusting to is the Chain Rod. Unlike the Triple Rod, it fires out as far as it can go in one shot, and can be used to hook onto objects and pull them in like a fishing line, such as the crate in the room. It also hooks onto the ceiling and can be used to swing back and forth. The further you extend it, the more momentum you can gain. The charge attack the Chain Rod has is the same with the Triple Rod's, but you need to level it up once to learn it. Cerveau will explain how the Chain Rod works if it seems too bizarre, so don't worry about getting confused with this weapon.
Visiting Ciel[edit]
Ciel is also waiting for you to pay a visit. Enter her room next. She's sitting at her desk at work, but immediately notices Zero. After asking how he is, she says Zero found the base before falling unconscious, but he doesn't recall coming anywhere near it. Ciel has spent the past year constantly working on a way to develop something equal to Energy Crystals and solve the energy crisis. While ruling, Neo Arcadia, Copy X started calling Reploids inferior, and had many scrapped so humans would have enough crystals available. Ciel sees this has occurred in past history. Knowing a substitute energy usually ends the conflict, she's studied to try and make one. Ciel is upset that Elpizo doesn't take her solution seriously, since he thinks Neo Arcadia must be defeated, but Ciel knowns the only real way for peace is through science. She decides to get back to work and offers to save your data, which is a very good idea about now. You can still talk to her, or ask about Cyber-Elves. This game lacks Trans Servers, so Ciel's the one to come to so you can feed and download Elves if you need to. There is also a strange Cyber-Elf in a capsule Ciel is studying. It happens to be from Elpizo, since he used to work in Neo Arcadia and had a chance to retrieve one just before joining the Resistance. For some reason, it's much more different from any normal Cyber-Elf.
If you've paid your visits to Ciel and Cerveau, then you need to check in with Elpizo and see what he's doing. He appears to be on the verge of something big...
Operation Righteous Strike[edit]
Upon returning to the command center, Zero will walk in during Elpizo's briefing with his troops. Elpizo is planning a guerilla assault on Neo Arcadia he calls, "Operation Righteous Strike." Elpizo's troops will attack the city while it's still vulnerable, since Copy X isn't around to rule it. The troops are stirred into even higher spirits after hearing him speak, and file out again.
After speaking to his troops, Elpizo turns his attention to Zero and keys him in on the impact this operation could have. If it succeeds, it will be a massive blow to Neo Arcadia and a morale boost to the Resistance. Even so, Zero is still doubtful on how well things will turn out, but even he can't convince Elpizo to change his mind. Elpizo does manage to recognize what Ciel told him about being too harsh. Elpizo shows interest in Zero's great skills and asks him to help out with his plans for the strike.
When Elpizo asks for your help, answer yes, and he will present you with four missions that have proven to be too difficult for his own troops to complete, as Mutos Reploids protect each area. The four are: Hyleg Ourobockle, Poler Kamrous, Phoenix Magnion, and Panter Flauclaws. Out of these missions, the easiest by far is "Rescue Reploids in the Forest of Dysis," Hyleg Ourobockle's area, and it houses a Sub Tank that can become insurance for the tougher missions, so you don't have to perilously rely on a tiny health bar. The hardest is "Destroy Power Reactors in the Power Room," Phoenix Magnion's area, but successfully completing it first will eliminate most of the Pantheon troops in the other areas and make the remaining missions easier.
There are also still more places in the New Resistance Base to visit if you would like, except many Resistance members have yet to arrive, and the elevator isn't working properly. There aren't any Cyber-Elves to miss yet, so you can start a mission right away. To make the missions ahead easier, it's imperative you go back into the Sand Wilderness and level up all your weapons to their max level beforehand. Otherwise, the weapons won't be at their full potential, resulting in a crippling handicap as you traverse harder missions- bad enough that it can get you killed easier and ruin your mission rankings.
You can choose any mission you like right now. One possible start is Hyleg Ourobockle, purely to take the edge of difficulty of the game by obtaining the Sub Tank after its completion. Another option is to start from Poler Kamous, who is the easiest of the four bosses, and leave Hyleg Ourobockle for after you obtain the Flame Chip, which is useful during his stage. Because Poler Kamrous is sluggish and pea-brained compared to many other clever, quick-footed Mutos Reploids, this is one choice to go first, because this boss will be the easiest due to their slow speed and slowed reaction time to your attacks. The gutsy option is to go for Phoenix Magnion first. Though intimidating, he is easy to keep control of given that he is purely reactionary to a point, and his stage is a perfect place to both obtain the mighty X Form and level up your weapons after the mission's completion on top of his defeat causing the aforementioned removal of several enemies in the other missions.
Exploring the Base after the first mission[edit]
3 cyber elves (Resistance Base):
Cyber-Elf Iteroth
Cyber-Elf Mikilar- Cyber-Elf Pireff
After you've accomplished the first mission, several new Resistance soldiers will have arrived, and the elevator will have been fixed. Ciel's computer will also have entrance data logged in it if you would like to visit her. Most importantly, you now have access to three Cyber-Elves.
Cyber-Elf #1[edit]
Head down to the first floor and enter the door marked 1F-B. You'll enter the storage room and meet the dull Reploid Autruche. Right behind him is a Cyber-Elf box with 
Cyber-Elf Iteroth inside. It is another Cyber-Elf that ensures all minor stage enemies drop items when defeated.
Cyber-Elf #2[edit]
Next, head up to the fifth floor and climb into the right turret to meet up with Dande, who has recovered completely since his rescue in the first game. Talk to him, and he'll give you a lost Cyber-Elf he found, 
Cyber-Elf Mikilar. Talk to him immediately after the first mission, because you can only get the Elf before you've completed all four missions. Dande will not bring up the Elf in conversation beyond that point of the game.
Upon use, this Cyber-Elf encircles Zero for about 30 seconds, absorbing any bullets that touch it. The bullets will be converted into Life Energy Capsules to replenish lost vitality. Sadly, the Cyber-Elf burns itself out by releasing its power, dying soon after its use. While it's still alive, the Elf races around Zero to shield him from bullets, but it isn't a foolproof defense; bullets can still slip past the Elf, and hurt Zero. Moreover, the Elf doesn't react to gunfire and automatically fly into the path of bullets. To lessen these issues, wait until you collect two or three Elves that share this power, and use them at the same time, because more Elves means more coverage against gunfire. A second viable strategy is to pair it up with an Elf that can attack enemies, subdue enemies, or eat enemy bullets.
Cyber-Elf #3[edit]
After you receive Mikilar, head up to the roof. Try to wall-jump over the side of the left gun turret. Waiting on the other end is another Cyber-Elf box with Cyber-Elf Pireff inside. This Elf restores eight bars of your Life Energy. If your life bar hasn't been upgraded, that amounts to half your health. As you enhance your life bar, this won't be as helpful in recovering your full HP. You can also sacrifice this Cyber-Elf to store life energy in a Sub Tank (obtainable later in the game), but because life energy is fairly easy to replenish, plus the possibility to get an EX Skill that makes it child's play (recieved in a forest-oriented mission), such is a waste of its power. It should only be used as a last resort, when you've lost nearly all your health and Sub Tank reserves, to save your skin before you get killed.