You get this one for defeating the penultimate boss Anubis.
FAQsimile put it better than I could hope to.
http://www.gamefaqs.com/ps2/561586-zone-of-the-enders-the-2n...SPOILERS
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| Anubis |--------------------------------------------------------
| Pilot: ??? |
|--------------------------------------------------------|
| You're once again fighting Anubis, and this time you |
| have to bring it down to half of its health in order |
| to proceed further. |
| This can be done fairly easily now that you have the |
| new upgrades and Jehuty Ver. 2. Use ZERO-SHIFT when |
| Anubis moves away, and just slash away using Melee, |
| and you should be fine. The battle will end shortly |
| and you'll move on. |
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Once you finish the battle, you'll see some more CUTSCENEs, then move on to
the next area.
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6.13 Compressed Space
=========================
When the CUTSCENEs end, you will be forced into yet another BOSS battle.
From here on out, there will be mainly BOSS fights, so be prepared to fight
hardcore.
--\\ NOTE \\---------------------------------------------
| During the CUTSCENE, ADA will inform you that many of |
| Jehuty's SUBWEAPONs and features are now destroyed. |
| This version of Jehuty is called Damaged Jehuty. |
| The only SUBWEAPONs you will have are ZERO-SHIFT and |
| GRAB; GRAB is not very useful. BURST, SLASH, and DASH |
| will be the only normal functions of Jehuty that you |
| will be able to use; hence, no long-range attacks |
| anymore. |
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| Anubis |--------------------------------------------------------
| Pilot: Nohman |
|--------------------------------------------------------|
| This is a tough battle. Anubis will be out of range |
| most of the time, and Jehuty is Damaged so you'll be |
| able to use ZERO-SHIFT as your only Subweapon. |
| The general pattern of this battle is as follows: |
| - Anubis appears, calls out, then disappears. |
| - Anubis reappears and fires a BURST attack. |
| After Anubis reappears, you can see him charging his |
| BURST attack. When he does this, you must DASH to |
| the side and avoid it, then use ZERO-SHIFT to get in |
| close to Anubis and begin using SLASH on him. |
| After a long, long time of doing this, after Anubis' |
| health is past halfway, his armor will break up some |
| and he will begin to focus more on battling you with |
| Melee Attacks rather than BURST. If you dodge first |
| then attack, you can sometimes slip in a hit or two. |
| You may also want to use a DASH-SLASH combo (hold R2 |
| and press Square) to hit him. |
| Once you get Anubis' health past 1/4th of the way, |
| more armor will shatter and he will focus more on |
| evading you and doing sharp, quick Melee Attacks. |
| Anubis may also use regular SHOT Attacks, which you |
| should use R1 DEFEND against. DASH away from them |
| if he begins to charge up a BURST. |
| Keep up the fight, and eventually, after a somewhat |
| long and tiring battle, you will defeat Anubis and |
| arrive on Phobos/Aumaan. |
| Don't throw the party just yet, you're not done. |
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