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* PolishedPort: ''Team Colonel'' came out after ''Team Protoman'', and has a few subtle changes that work to its benefit for it. Several of the weaker Navis in Liberation missions got buffed over their ''Team Protoman'' counterparts, ''especially'' [=ToadMan=] when compared to Meddy, and Team Colonel just overall has better synergy in their abilities than Team Protoman and operate more efficiently together. In terms of story, it's a mixed bag of pros and cons for switching Chaud and Barrel's roles, but at the least ''Team Colonel'' has an expanded ending that explains [[spoiler:Dr. Regal's reformation]], and TheReveal that [[spoiler:Wily is alive]] acts as a SequelHook for the next game.

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* PolishedPort: ''Team Colonel'' came out after ''Team Protoman'', [=ProtoMan=]'', and has a few subtle changes that work to its benefit for it. Several of the weaker Navis in Liberation missions got buffed over their ''Team Protoman'' [=ProtoMan=]'' counterparts, ''especially'' [=ToadMan=] when compared to Meddy, and Team Colonel just overall has better synergy in their abilities than Team Protoman [=ProtoMan=] and operate more efficiently together. In terms of story, it's a mixed bag of pros and cons for switching Chaud and Barrel's roles, but at the least ''Team Colonel'' has an expanded ending that explains [[spoiler:Dr. Regal's reformation]], and TheReveal that [[spoiler:Wily is alive]] acts as a SequelHook for the next game.



* ThatOneSidequest: The final liberation mission in Nebula Area 5. While the previous two Nebula missions were difficult, they were at least fair. The last one however has the entire field sectioned off by three stages of barrier panels, creating an almost entirely linear path that leaves you little opportunity to strategize or explore, reducing progress to crawling your way towards the barrier keys one tile at a time. While you have [=GyroMan=] / [=ShadowMan=] to scout ahead, the key paths are all blocked by viruses and dark holes they can't cross, so they can't use their main strength effectively. The first key to begin the chain is hidden behind [=BlizzardMan=], who appears alongside [=CosmoMan=] but both are in their V3 forms. Thus not only do you need to fight two bosses, but the map is laid out in such a way that the path to [=BlizzardMan=] crosses both their zones of attack. Speaking of which, the viruses in the map will teleport over the barriers to get you as you pass them, and include Swordies who will probably teleport right in front of you, blocking the path and making you waste a turn killing them. And since you're in the depths of the BonusDungeon, the V3 viruses will make 1-turn liberations very difficult. All of this combined makes the finale to the liberation missions a slog to grind through. [=ToadMan=]'s SequenceBreaking ability in ''Team Colonel'' greatly alleviates a lot of the tedium involved, but ''Team Protoman'' has to do things the hard way.
* TheyWastedAPerfectlyGoodCharacter: [=GutsMan=], Roll, and Glyde are dismissed from the story within the first hour of the game when Nebula steals the trio's [=PETs=], and Lan's friends spend the rest of the game moping about it unable to do anything (though Mayl at least gives you the Roll series again). This is particularly glaring when you get to the Undernet scenario of ''Team Protoman'' and meet Meddy, a medic Navi whose healing powers can help negate dark power, and her Soul Union is performed with healing chips. Considering the ''Battle Network 4: Red Sun'' had made Roll an opponent and she gave the Soul Union for healing chips, why write her out of the story for this game and then introduce a new character with the same abilities to fill the same role?

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* ThatOneSidequest: The final liberation mission in Nebula Area 5. While the previous two Nebula missions were difficult, they were at least fair. The last one however has the entire field sectioned off by three stages of barrier panels, creating an almost entirely linear path that leaves you little opportunity to strategize or explore, reducing progress to crawling your way towards the barrier keys one tile at a time. While you have [=GyroMan=] / [=ShadowMan=] to scout ahead, the key paths are all blocked by viruses and dark holes they can't cross, so they can't use their main strength effectively. The first key to begin the chain is hidden behind [=BlizzardMan=], who appears alongside [=CosmoMan=] but both are in their V3 forms. Thus not only do you need to fight two bosses, but the map is laid out in such a way that the path to [=BlizzardMan=] crosses both their zones of attack. Speaking of which, the viruses in the map will teleport over the barriers to get you as you pass them, and include Swordies who will probably teleport right in front of you, blocking the path and making you waste a turn killing them. And since you're in the depths of the BonusDungeon, the V3 viruses will make 1-turn liberations very difficult. All of this combined makes the finale to the liberation missions a slog to grind through. [=ToadMan=]'s SequenceBreaking ability in ''Team Colonel'' greatly alleviates a lot of the tedium involved, but ''Team Protoman'' [=ProtoMan=]'' has to do things the hard way.
* TheyWastedAPerfectlyGoodCharacter: [=GutsMan=], Roll, and Glyde are dismissed from the story within the first hour of the game when Nebula steals the trio's [=PETs=], and Lan's friends spend the rest of the game moping about it unable to do anything (though Mayl at least gives you the Roll series again). This is particularly glaring when you get to the Undernet scenario of ''Team Protoman'' [=ProtoMan=]'' and meet Meddy, a medic Navi whose healing powers can help negate dark power, and her Soul Union is performed with healing chips. Considering the ''Battle Network 4: Red Sun'' had made Roll an opponent and she gave the Soul Union for healing chips, why write her out of the story for this game and then introduce a new character with the same abilities to fill the same role?

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* SurprisinglyImprovedSequel: Given how ''Mega Man Battle Network 4'' turned out not many were expecting much from the fifth installment. Not only is 5 considered to be a massive improvement in story and gameplay, but offers way more innovation to the series than 4 ever did.


* {{Woolseyism}}: An ''attempted'' one that turned into a BlindIdiotTranslation. The creatures atop End Castle are ''shachihoko'', a mythical Japanese animal often used as roof adornments in architecture. The translators replaced this word with Gargoyle, which fits perfectly as an English equivalent of the shachihoko that Western audiences will recognize better. The problem is that characters refer to the structures atop End Castle as Gargoyles while saying in the same scene (sometimes even in the same line of dialogue) that they look like fish. This results in some very bizarre dialogue where the entire cast seems to think that gargoyles look like giant fish.

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* {{Woolseyism}}: An ''attempted'' one that turned into a BlindIdiotTranslation. The creatures atop End Castle are ''shachihoko'', a mythical Japanese fish-like animal often used as roof adornments in architecture. The translators replaced this word with Gargoyle, which fits perfectly as an English equivalent of the shachihoko that Western audiences will recognize better. The problem is that characters refer to the structures atop End Castle as Gargoyles while saying in the same scene (sometimes even in the same line of dialogue) that they look like fish. This results in some very bizarre dialogue where the entire cast seems to think that gargoyles look like giant fish.


** [=NumberMan=] is seen as the weakest member of the Team Colonel cast. His Charge Shot, like Meddy's, is a lobbed bomb with variable damage that can whiff if it makes direct contact with an enemy, and his unique chip is not as useful as the others when it is dependent on enemy movement. His Number Check ability can collect items and break traps without putting him into combat, but it pales in comparison to [=SearchMan's=] ability which can liberate up to entire lines of item and trap panels.

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** [=NumberMan=] is seen as the weakest member of the Team Colonel cast. His Charge Shot, like Meddy's, is a lobbed bomb with variable damage that can whiff if it makes direct contact with an enemy, and his unique chip is not as useful as the others when it is dependent on enemy movement. His Number Check ability can collect items and break traps without putting him into combat, but it pales in comparison to [=SearchMan's=] ability which can liberate up to entire lines of item and trap panels.panels.
* {{Woolseyism}}: An ''attempted'' one that turned into a BlindIdiotTranslation. The creatures atop End Castle are ''shachihoko'', a mythical Japanese animal often used as roof adornments in architecture. The translators replaced this word with Gargoyle, which fits perfectly as an English equivalent of the shachihoko that Western audiences will recognize better. The problem is that characters refer to the structures atop End Castle as Gargoyles while saying in the same scene (sometimes even in the same line of dialogue) that they look like fish. This results in some very bizarre dialogue where the entire cast seems to think that gargoyles look like giant fish.


** The beginning of Battle Network 5 has Dr. Hikari send Lan into his office to retrieve something. When Lan sets foot into the office, Regal and his goons throw a gas bomb into the room knocking everyone unconscious, including Lan. Regal kidnaps Dr. Hikari and takes away Mayl, Dex, and Yai's [=PET=]s and wonders where Lan is, not thinking to check Dr. Hikari's office which is in the same room. If he had checked and taken away Mega Man as well, 5 could've turned out differently.

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** The beginning of Battle Network 5 has game opens with Lan and his friends visiting his father's office, and when Dr. Hikari send sends Lan into to get something from his office to retrieve something. When Lan sets foot into the office, desk, Regal and his goons throw a gas bomb into gases the room knocking everyone unconscious, including Lan. Regal kidnaps and abducts Dr. Hikari Hikari, and also takes away the [=PETs=] of Mayl, Dex, and Yai's [=PET=]s Yai. Lan is overlooked because he was at the desk and wonders Nebula's agents don't see him. The problem is that the desk is segmented off from the rest of the room by a cubicle wall, and the way the scene is set up with where Nebula agents stand and how Lan is, not thinking has collapsed, you can't even say he's in their peripheral vision, he's pretty much right in front of them a few feet away and to check the side. If Dr. Hikari's office which is in Regal just looked around the same room. If he room for a few seconds, or if his agents could see more than six inches in front of them, Lan would have had checked and his PET taken away Mega Man as well, 5 could've turned and the game's events would have played out differently. very differently.


* ContestedSequel: The fifth game is the most polarizing.
** The positives:
*** Better story than ''Battle Network 4's'' ExcusePlot TournamentArc.
*** Dark Chips have increased utility.
*** [[NewGamePlus Multiple playthroughs]] are no longer needed.
** The negatives:
*** "Better than [=BN4=]" [[DamnedByFaintPraise is hardly a grand achievement]].
*** [[UnexpectedGameplayChange Liberation Missions]] are contentious and undercooked gameplay segments that rely increasingly on FakeDifficulty.
*** The game retains the contentious changes to the battle system from ''4'', namely the nerfing of battlechips and Program Advances in favor of gameplay balance focusing on Soul Unisons and their unique abilities.

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* ContestedSequel: The fifth game is the most polarizing.
** The positives:
*** Better story
polarizing in the series. While it has better reception than ''Battle Network 4's'' ExcusePlot TournamentArc.
*** Dark Chips have increased utility.
*** [[NewGamePlus Multiple playthroughs]] are no longer needed.
** The negatives:
*** "Better than [=BN4=]" [[DamnedByFaintPraise is hardly a grand achievement]].
*** [[UnexpectedGameplayChange Liberation Missions]] are contentious and undercooked
''4'', near-universally agreed to be the weakest entry in the series, ''5'' still holds onto many of the gameplay segments that rely increasingly on FakeDifficulty.
*** The game retains the contentious
changes to the battle system that occurred going from ''3'' to ''4'', namely the nerfing of battlechips and Program Advances in favor of gameplay balance focusing on Soul Unisons and their unique abilities.abilities. The story is also better regarded than ''4's'' ExcusePlot TournamentArc, but still not all that great compared to the stories of earlier games.


* ContestedSequel: While it has better reception than ''4'', near-universally agreed to be the weakest entry in the series, ''5'' still holds onto many of the gameplay changes that occurred going from ''3'' to ''4'', namely the nerfing of battlechips and Program Advances in favor of gameplay balance focusing on Soul Unisons and their unique abilities. The story is also better regarded than ''4's'' ExcusePlot TournamentArc, but still not all that great compared to the stories of earlier games.

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* ContestedSequel: While it has better reception The fifth game is the most polarizing.
** The positives:
*** Better story
than ''4'', near-universally agreed to be the weakest entry in the series, ''5'' still holds onto many of the ''Battle Network 4's'' ExcusePlot TournamentArc.
*** Dark Chips have increased utility.
*** [[NewGamePlus Multiple playthroughs]] are no longer needed.
** The negatives:
*** "Better than [=BN4=]" [[DamnedByFaintPraise is hardly a grand achievement]].
*** [[UnexpectedGameplayChange Liberation Missions]] are contentious and undercooked
gameplay segments that rely increasingly on FakeDifficulty.
*** The game retains the contentious
changes that occurred going to the battle system from ''3'' to ''4'', namely the nerfing of battlechips and Program Advances in favor of gameplay balance focusing on Soul Unisons and their unique abilities. The story is also better regarded than ''4's'' ExcusePlot TournamentArc, but still not all that great compared to the stories of earlier games.abilities.



* IdiotPlot: The clue that eventually leads to the {{Macguffin}} Regal is searching for is found on Dr. Hikari's computer when Lan and [=MegaMan=] check it late in the game. This immediately invites the FridgeLogic that ''no one checked his computer themselves''; neither Nebula, who kidnapped him for information they believe he knows, nor the officials, who are investigating why Nebula would kidnap him. If either group had the thought to just check his personal files earlier in the game, they could have found the {{Macguffin}} within a few hours.

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* IdiotPlot: IdiotPlot:
** The beginning of Battle Network 5 has Dr. Hikari send Lan into his office to retrieve something. When Lan sets foot into the office, Regal and his goons throw a gas bomb into the room knocking everyone unconscious, including Lan. Regal kidnaps Dr. Hikari and takes away Mayl, Dex, and Yai's [=PET=]s and wonders where Lan is, not thinking to check Dr. Hikari's office which is in the same room. If he had checked and taken away Mega Man as well, 5 could've turned out differently.
**
The clue that eventually leads to the {{Macguffin}} Regal is searching for is found on Dr. Hikari's computer when Lan and [=MegaMan=] check it late in the game. This immediately invites the FridgeLogic that ''no one checked his computer themselves''; neither Nebula, who kidnapped him for information they believe he knows, nor the officials, who are investigating why Nebula would kidnap him. If either group had the thought to just check his personal files earlier in the game, they could have found the {{Macguffin}} within a few hours.


** The inability to use Program Advances more than once per battle. This resulted in the mechanic, which was the basis of many folders in previous games, to lose virtually all of its usefulness.
** Flinching. An overwhelming amount of chips in this game give the enemy invincibility frames upon connecting, pretty much mandating the use of chips like Blinder to circumvent this.

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** The inability to use Program Advances more than once per battle. This resulted in The result was that the mechanic, which was the basis of many folders in previous games, to lose lost virtually all of its usefulness.
usefulness in this one.
** Flinching. An overwhelming amount of chips in this game give the enemy invincibility frames upon connecting, pretty much mandating the use of chips like making it mandatory to have Blinder in your folder to circumvent this.speed up battles.

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* ComplacentGamingSyndrome: The S-code is almost unanimously seen as the optimal code to base a folder around, as it offers some great offensive chips (Cactus Ball, Drill Arm and Super Vulcan, to name a few), which synergize with [=PA=]s like Wild Bird, Big Noise and Life Sword.


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* ScrappyMechanic:
** The inability to use Program Advances more than once per battle. This resulted in the mechanic, which was the basis of many folders in previous games, to lose virtually all of its usefulness.
** Flinching. An overwhelming amount of chips in this game give the enemy invincibility frames upon connecting, pretty much mandating the use of chips like Blinder to circumvent this.


** The [=NumberMan=] Soul Unison, the ''Team Colonel'' equivalent, is just as breaking. It automatically gives you ''ten'' chips in the Custom window and all your neutral chips get +10 ATK. This makes it very easy to get the chips you need to form a powerful combo.
** It's no mystery that the Chaos Unisons are PurposelyOverpowered, as your Charge Shot becomes the Dark Chip without any side effects. The supposed drawback can be bypassed with PauseScumming, so you can fire off incredibly strong attacks in a single turn to trivialize most encounters. They have much less utility in Liberation Missions, though, since you're forced to have less time with the Chaos Unison during a liberation battle and your teammates cannot tap into this power.

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** The [=NumberMan=] Soul Unison, the ''Team Colonel'' equivalent, Unison is just as breaking. broken as Search Soul. It automatically gives you ''ten'' chips in the Custom window and all your neutral chips get +10 ATK. This makes window, making it very easy to get the chips you need to form a powerful combo.
** It's no mystery that
combo. It also grants all your neutral chips +10 ATK, effectively doubling the damage dealt by the infamous Vulcan chips. The soul's only downside is its utterly terrible Charge Shot, but given its combo potential, it's unlikely you'll be using your buster anyways.
** The
Chaos Unisons are PurposelyOverpowered, as change your Charge Shot becomes into the Dark Chip used to enter them, without triggering any of their negative side effects. The supposed drawback is that mistiming the shot summons an invincible enemy on the opposite side of the field, but that can be bypassed with PauseScumming, so allowing you can to fire off incredibly strong attacks in a single turn to trivialize most encounters. They have much less utility in Liberation Missions, though, since you're forced to have less time with the Chaos Unison during a liberation battle battle, and your teammates cannot tap into this power.



*** Shadow Chaos has Dark Invis, which turns [=MegaMan=] fully invincible but uncontrollable as he jumps around the battlefield, firing buster shots and using previous chips attacks or even Program Advances at random. In situtations where your Busting Rank doesn't matter, you can spam Dark Invis all fight and hope that enough hits connect to finish off the enemy.

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*** Shadow Chaos has Dark Invis, which turns [=MegaMan=] fully invincible but uncontrollable as he jumps around the battlefield, firing buster shots and using previous chips attacks or even Program Advances at random. In situtations situations where your Busting Rank doesn't matter, you can spam Dark Invis all fight and hope that enough hits connect to finish off the enemy.


* BrokenBase
** '''Liberation missions'''. Some players enjoy them for the UnexpectedGameplayChange providing a new type of challenge, and you get to play as different Navis with their own strengths and weaknesses. Others hate them because they're tedious, contain FakeDifficulty, and need to be approached differently from normal battles because the flow of combat is different (trying to defeat all enemies in one turn with various different Navis, instead of using Soul Unisons to put together combos of chips). Defenders of liberation missions also point out that the pattern of "subplot, recruit new Navi, liberation mission" may be dull, but it's more fun than some of the minigames and puzzles used in previous games that were their own kind of tedium. It's even been said that how much you like ''Battle Network 5'' can be directly correlated to how much you liked the liberation missions.

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* BrokenBase
**
BrokenBase: '''Liberation missions'''. Some players enjoy them for the UnexpectedGameplayChange providing a new type of challenge, and you get to play as different Navis with their own strengths and weaknesses. Others hate them because they're tedious, contain FakeDifficulty, and need to be approached differently from normal battles because the flow of combat is different (trying to defeat all enemies in one turn with various different Navis, instead of using Soul Unisons to put together combos of chips). Defenders of liberation missions also point out that the pattern of "subplot, recruit new Navi, liberation mission" may be dull, but it's more fun than some of the minigames and puzzles used in previous games that were their own kind of tedium. It's even been said that how much you like ''Battle Network 5'' can be directly correlated to how much you liked the liberation missions.

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* AccidentalInnuendo: "I'll jack in to your squirrel if that's what it takes."


** Skully viruses will throw bones that move very slowly towards you one panel at a time, making it very difficult to avoid them when they're fought alongside other viruses. However, the true annoyance is that when hit with any powerful attack above a standard buster shot, they collapse into a pile of bones and become immune to damage for several seconds until they reform. In normal fights a Skully can tank your time and bursting rank, but in liberation missions the sight of a Skully is your cue to kiss your one-turn liberation goodbye.

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** Skully viruses will throw bones that move very slowly towards you one panel at a time, making it very difficult to avoid them when they're fought alongside other viruses. However, the true annoyance is that when hit with any powerful attack above a standard buster shot, they collapse into a pile of bones and become immune to damage for several seconds until they reform. In normal fights a Skully can tank your time and bursting busting rank, but in liberation missions the sight of a Skully is your cue to kiss your one-turn liberation goodbye.


** [=SearchMan=]'s Soul Unison power is to "shuffle" your currently available battle chips, up to three times a turn. You can do this even while selecting a chip to use and then shuffling the rest to keep that chip on standby. This makes it ''ridiculously'' easy to get the chips you need every turn, and adding in Custom+ programs to boost the number of chips you get each turn just makes it easier.

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** [=SearchMan=]'s Soul Unison power is to "shuffle" your currently available battle chips, up to three times a turn. You can do this even while selecting a chip to use and then shuffling the rest to keep that chip on standby. This makes it ''ridiculously'' easy to get the chips you need every turn, and adding in Custom+ programs to boost the number of chips you get each turn just makes it easier. The Soul's only downside is that the Cursor chips required to enter it are either situational or downright terrible on their own.



*** With Number Chaos, your charged shot gives your next chip +50 ATK; multi-hitting chips will hit as hard as Program Advances, and the Infinite Vulcan Program Advance will ''shred'' a boss.
* GoodBadBugs: [=ToadMan=]'s order point ability makes a Navi's next liberation liberate five panels in a line ahead of them. Unlike other abilities like this, this ability can [[SequenceBreaking bypass barrier panels]] and liberate dark panels other Navis and abilities can't reach. While this has limited usage in most missions, it makes the final liberation mission in Nebula Area 5 a total joke. [[ThatOneSidequest No one is complaining about this]].

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*** With Number Chaos, your charged shot gives your next chip +50 ATK; multi-hitting ATK. Multi-hitting chips will hit as hard as Program Advances, and the Infinite Vulcan Program Advance will ''shred'' a boss.
* GoodBadBugs: GoodBadBugs:
**
[=ToadMan=]'s order point ability makes a Navi's next liberation liberate five panels in a line ahead of them. Unlike other abilities like this, this ability can [[SequenceBreaking bypass barrier panels]] and liberate dark panels other Navis and abilities can't reach. While this has limited usage in most missions, it makes the final liberation mission in Nebula Area 5 a total joke. [[ThatOneSidequest No one is complaining about this]].this]].
** In the Japanese version of ''Team [=ProtoMan=]'', selecting "No" when Meddy asks if the player wants to use Twin Liberation will trigger the ability anyways, without consuming Order Points. To make it even better, the glitch bypasses the first battle, meaning all it takes to liberate an entire row of panels is to destroy the one on the opposite end of Meddy.



** Skully viruses will throw bones that move very slowly and move towards you one panel at a time, making it very difficult to avoid them when they're fought alongside other viruses. However, the true annoyance is that when hit with any powerful attack above a standard buster shot, they collapse into a pile of bones and become immune to damage for several seconds until they reform. In normal fights a Skully can tank your time and busting rank, and in liberation missions, the sight of a Skully is your cue to kiss your one-turn liberation goodbye.

to:

** Skully viruses will throw bones that move very slowly and move towards you one panel at a time, making it very difficult to avoid them when they're fought alongside other viruses. However, the true annoyance is that when hit with any powerful attack above a standard buster shot, they collapse into a pile of bones and become immune to damage for several seconds until they reform. In normal fights a Skully can tank your time and busting bursting rank, and but in liberation missions, missions the sight of a Skully is your cue to kiss your one-turn liberation goodbye.



* IdiotPlot: The clue that eventually leads to the {{Macguffin}} Regal is searching for is found on Dr. Hikari's computer when Lan and [=MegaMan=] check it late in the game. This immediately invites the FridgeLogic that ''no one checked his computer themselves''; neither Nebula, who kidnapped him for information they believe he knows, nor the officials, who are investigating while Nebula would kidnap him. If either group had the thought to just check his personal files earlier in the game, they could have found the {{Macguffin}} within a few hours.

to:

* IdiotPlot: The clue that eventually leads to the {{Macguffin}} Regal is searching for is found on Dr. Hikari's computer when Lan and [=MegaMan=] check it late in the game. This immediately invites the FridgeLogic that ''no one checked his computer themselves''; neither Nebula, who kidnapped him for information they believe he knows, nor the officials, who are investigating while why Nebula would kidnap him. If either group had the thought to just check his personal files earlier in the game, they could have found the {{Macguffin}} within a few hours.



* ThatOneLevel: The second teammate scenario, with [=GyroMan=] / [=ShadowMan=]; it's basically this game's answer to ''[=BN3=]'s'' [=BubbleMan=] scenario ''and'' the same game's Hospital Comp area. The net is full is clouds that you need the Vacuum Program to suck up, but you can only suck in up to ten units before you need to run to a Mr. Prog to recharge. While it's fine at first, as you progress the clouds start taking up more units to suck up, the Mr. Progs go from infinite recharges of the vacuum to one-time uses, and then to just partial recharges, effectively making the area a puzzle where if you don't suck up the right clouds to open the path, you have to backtrack all the way to the start of the area to empty the vacuum. And to add insult to injury, after you catch up to [=GyroMan=] / [=ShadowMan=] in each area, he pauses to taunt you before running off and making you chase him. When you finally corner him and he fights you, savor the opportunity to beat his face in.

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* ThatOneLevel: The second teammate scenario, with [=GyroMan=] / [=ShadowMan=]; it's [=ShadowMan=], is basically this game's answer to ''[=BN3=]'s'' [=BubbleMan=] scenario ''and'' the same game's Hospital Comp area. The net is full is of clouds that you need the Vacuum Program to suck up, but you can only suck in up to ten units before you need to run to a Mr. Prog to recharge. While it's fine at first, as you progress the clouds start taking up more units to suck up, the Mr. Progs go from infinite recharges of the vacuum to one-time uses, and then to just partial recharges, effectively making the area a puzzle where if you don't suck up the right clouds to open the path, you have to backtrack all the way to the start of the area to empty the vacuum. And to add insult to injury, after you catch up to [=GyroMan=] / [=ShadowMan=] in each area, he pauses to taunt you before running off and making you chase him. When you finally corner him and he fights you, savor the opportunity to beat his face in.


*** Further, the Dark Circle Dark Chip has a seven-square targeted shot as its charge shot, dealing 300 damage to all enemies it hits. However, if the enemy is Area Grabbed, leaving them with six panels, the seventh targeted square will overlap the first and the shot will deal two hits. If you can Area Grab the enemy twice you can pretty much guarantee yourself two hits, and if the enemy is in the center panel and you stop the cursor right on them, they'll get hit ''four times''.
** The [=NumberMan=] Soul Unison, the ''Team Colonel'' equivalent, is just as breaking. It automatically gives you ''ten'' chips in the Custom window and all your chips get +10 ATK. This makes it very easy to get the chips you need and they'll all get a power boost. With Chaos Number Soul, you can use a charged shot to give your next chip +50 ATK; multi-hitting chips will hit as hard as Program Advances.
* GoodBadBugs: [=ToadMan=]'s order point ability makes a Navi's next liberation liberate four panels in a line ahead of them. Unlike other abilities like this, this ability can bypass barrier panels and liberate dark panels other Navis and abilities can't reach. While this has limited usage in most missions, it makes the final liberation mission in Nebula Area 5 a total joke. [[ThatOneSidequest No one is complaining about this]].
* GoddamnBats: Skully viruses will throw bones that move very slowly and move towards you one panel at a time, making it very difficult to avoid them when they're fought alongside other viruses. However, the true annoyance is that when hit with any powerful attack above a standard buster shot, they collapse into a pile of bones and become immune to damage for several seconds until they reform. In normal fights a Skully can tank your time and busting rank, and in liberation missions, the sight of a Skully is your cue to kiss your one-turn liberation goodbye.

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*** Further, ** The [=NumberMan=] Soul Unison, the Dark Circle ''Team Colonel'' equivalent, is just as breaking. It automatically gives you ''ten'' chips in the Custom window and all your neutral chips get +10 ATK. This makes it very easy to get the chips you need to form a powerful combo.
** It's no mystery that the Chaos Unisons are PurposelyOverpowered, as your Charge Shot becomes the
Dark Chip without any side effects. The supposed drawback can be bypassed with PauseScumming, so you can fire off incredibly strong attacks in a single turn to trivialize most encounters. They have much less utility in Liberation Missions, though, since you're forced to have less time with the Chaos Unison during a liberation battle and your teammates cannot tap into this power.
*** Proto Chaos and Toad Chaos are very strong Chaos Unisons with high-damage wide-area attacks. They only become available in the last few chapters of the game, but once you gain access to them they easily level many virus encounters.
*** Knight Chaos has Dark Drill, which is a stronger and longer-lasting version of your standard Drill Arm chips. When used on a target that can't get pushed back further, they end up taking five to six 100-damage hits, letting you pulverize bosses after a single Area Grab.
*** Shadow Chaos has Dark Invis, which turns [=MegaMan=] fully invincible but uncontrollable as he jumps around the battlefield, firing buster shots and using previous chips attacks or even Program Advances at random. In situtations where your Busting Rank doesn't matter, you can spam Dark Invis all fight and hope that enough hits connect to finish off the enemy.
*** Search Chaos
has a seven-square targeted shot as its charge shot, dealing 300 damage to all enemies it hits. However, if the enemy is Area Grabbed, leaving them with six panels, the seventh targeted square will overlap the first and the shot will deal two hits. If you can Area Grab the enemy twice you can pretty much guarantee yourself two hits, and if the enemy is in the center panel and you stop the cursor right on them, they'll get hit ''four times''.
** The [=NumberMan=] Soul Unison, the ''Team Colonel'' equivalent, is just as breaking. It automatically gives you ''ten'' chips in the Custom window and all your chips get +10 ATK. This makes it very easy to get the chips you need and they'll all get a power boost. *** With Chaos Number Soul, you can use a Chaos, your charged shot to give gives your next chip +50 ATK; multi-hitting chips will hit as hard as Program Advances.
Advances, and the Infinite Vulcan Program Advance will ''shred'' a boss.
* GoodBadBugs: [=ToadMan=]'s order point ability makes a Navi's next liberation liberate four five panels in a line ahead of them. Unlike other abilities like this, this ability can [[SequenceBreaking bypass barrier panels panels]] and liberate dark panels other Navis and abilities can't reach. While this has limited usage in most missions, it makes the final liberation mission in Nebula Area 5 a total joke. [[ThatOneSidequest No one is complaining about this]].
* GoddamnBats: GoddamnedBats:
** The Lark series of viruses -- those that drop the Wide Shot chips -- fire shots that cover a wide area in battle. Mercifully, they never attack when they're in the middle row, else their attack is undodgeable. Not so mercifully, the wide coverage of these attacks make them notorious for breaking in-battle Mystery Data, sometimes ''within the very first second of the fight''.
**
Skully viruses will throw bones that move very slowly and move towards you one panel at a time, making it very difficult to avoid them when they're fought alongside other viruses. However, the true annoyance is that when hit with any powerful attack above a standard buster shot, they collapse into a pile of bones and become immune to damage for several seconds until they reform. In normal fights a Skully can tank your time and busting rank, and in liberation missions, the sight of a Skully is your cue to kiss your one-turn liberation goodbye.goodbye.
** Appley viruses pretty much serve to ruin a player's attempt at S-ranks or 1-turn Liberations. Most of the time they reside in their shell, only being vulnerable when emerging to attack. The shell makes them ''immune to everything but Fire attacks''. Not even Breaking attacks work on them. Also, if somehow they are killed first, they heal the other viruses.



* ThatOneSidequest: The final liberation mission in Nebula Area 5. While the previous two Nebula missions were difficult, they were at least fair. The last one however has the entire field sectioned off by three stages of barrier panels, creating an almost entirely linear path that leaves you little opportunity to strategize or explore, reducing progress to crawling your way towards the barrier keys one tile at a time. While you have [=GyroMan=] / [=ShadowMan=] to scout ahead, the key paths are all blocked by viruses and dark holes they can't cross, so they can't use their main strength effectively. The first key to begin the chain is hidden behind [=BlizzardMan=], who appears alongside [=CosmoMan=] but both are in their V3 forms. Thus not only do you need to fight two bosses, but the map is laid out in such a way that the path to [=BlizzardMan=] crosses both their zones of attack. Speaking of which, the viruses in the map will teleport over the barriers to get you as you pass them, and include Swordies who will probably teleport right in front of you, blocking the path and making you waste a turn killing them. All of this combined makes the finale to the liberation missions a slog to grind through. ''Team Colonel'' version completely reversed this and made it winnable within four turns thanks to [=ToadMan=]'s ability, but ''Team Protoman'' has to do things the hard way.

to:

* ThatOneSidequest: The final liberation mission in Nebula Area 5. While the previous two Nebula missions were difficult, they were at least fair. The last one however has the entire field sectioned off by three stages of barrier panels, creating an almost entirely linear path that leaves you little opportunity to strategize or explore, reducing progress to crawling your way towards the barrier keys one tile at a time. While you have [=GyroMan=] / [=ShadowMan=] to scout ahead, the key paths are all blocked by viruses and dark holes they can't cross, so they can't use their main strength effectively. The first key to begin the chain is hidden behind [=BlizzardMan=], who appears alongside [=CosmoMan=] but both are in their V3 forms. Thus not only do you need to fight two bosses, but the map is laid out in such a way that the path to [=BlizzardMan=] crosses both their zones of attack. Speaking of which, the viruses in the map will teleport over the barriers to get you as you pass them, and include Swordies who will probably teleport right in front of you, blocking the path and making you waste a turn killing them. And since you're in the depths of the BonusDungeon, the V3 viruses will make 1-turn liberations very difficult. All of this combined makes the finale to the liberation missions a slog to grind through. [=ToadMan=]'s SequenceBreaking ability in ''Team Colonel'' version completely reversed this and made it winnable within four turns thanks to [=ToadMan=]'s ability, greatly alleviates a lot of the tedium involved, but ''Team Protoman'' has to do things the hard way.

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