Secret Boss

Get to level 100 and collect all Navis chips. Then, go to Den Area 3 to access the warp to the secret Boss.

Combos

Combine the following chips in order to create the corresponding Program Advance:

Big Heart: Repair + Recov300 + Roll 
Double Hero: CustSwrd + VarSwrd + ProtoMan 
Dream Sword 1: Sword + WideSwrd + LongSwrd 
Dream Sword 2: FireSwrd + AquaSwrd + ElecSwrd 
Dream Sword 3: FireBlde + AquaBlde + ElecBlde 
Giga Burst: Spreader + Bubbler + HeatShot 
Greatest Bomb: LilBomb + CrosBomb + BigBomb 
Guts Shoot: MetGuard + DashAtk + GutsMan 
Machine Punch: GutPunch + ColdPnch + DashAtk 
Star Shower: SoniSlsh + GravHold + StarArro 
Stream Arrow: DoubNdl + TripNdl + QuadNdl 
Zero Counter: HiGuard + ZetSaber + Zero 
Zeta Cannon: Cannon + HiCannon + M-Cannon 
Zeta Ratton: Ratton1 + Ratton2 + Ratton3 

Defeating Guts Man

Have Roll, Vgun, Shotgun, and Cannons. First use Roll, then let him attack. Dodge it, then use any Shotgun, Vgun, or Cannons. When he attacks again, dodge it then attack. Do this rapidly to win and get the battle chip Gutspunch.

Defeating Gravity Man

While on your way to the Zero Account, you will discover many tough enemies, including Gravity Man. This Navi can be very difficult to defeat. Make sure that you have at least a few Half Energy Subchips (useful when low on health). Also, make sure to have a lot of projectile weapons, such as Cannon, Hi Cannon, Shotgun, etc. When you begin to fight him, you will find that his main weapon are energy balls. To dodge these, jump up and down. You will switch between standing on the ceiling and ground. Then, when the time is correct, use a projectile weapon. If your health gets low, use a Half Energy.

Defeating Fire Man

Have Water attacks and plenty of Swords. First, weaken him with Aqua attacks. Next, use a Sword attack. The moment you use it, jump backwards and dodge his body flame. Do this rapidly and win the battle 2 by 4. First, destroy a lot of viruses in Lan's computer. Jack in and out several times until you have 3,000 Zenny. Go to Higsbie's store and buy at least two AquaSwrds (three recommended).

Defeating Bright Man

Have a lot of GuardInvis, HighGuard, ShldGuard, and Guard chips. He has a shield. In order to do damage, you must hit him after he does a attack. The Guard and related chips will turn his attacks in to shock waves and send them at him. He will not reflect them. Do this numerous amount of times to defeat Bright Man.

Defeating Bass

Before attempting this, have five Invisibility Level 3. Go to Battle Simulator at the park and get all the opponents' Navi chips, including Proto Man. You wll get an email from Mayl, telling you about an extremely powerful Navi that was spotted at Den Area 3. In order to battle, you must have several double jumps, five Color Man Navi chips, M Cannon (as well as other projectile weaponry), and all the armors. Go to the teleporter that leads from Den Area 3 to Global Area 1. Use multiple double jumps to go to the top right ledge. Pick up the Slasher on the way up. Enter the green teleporter when you are ready. A Navi in a cloak will appear and attack. Do not toy with him. If you have Color Man, use it immediately to get rid of his energy shield, which also determines his elemental attacks. He attacks mainly with Seeker Energy. When his shield is down from Color Man or the opposite element to his shield, attack with Projectile chips; regular and charged attacks have no effect. About a quarter of the way through his HP, the battle will end and you will receive the Bass Navi chip (Attack 60, MP 64, attacks all enemies on screen and destroys shields). He cannot be fought again.

Duplicating Navi Chips

If you wish to have more than just one Nav Chipi, go to the Net Battle Simulator. Battle any Navi you wish to have. However, in order to get that Navi you cannot use a Navi Chip in battle. You can only use regular Battle Chips and Restore Chips. Also, you must defeat the Navi quickly. This works best with Fire Man, Guts Man, Ice Man, and Color Man. It is difficult to get other chips because some of the Bosses take too long to defeat.