Kirkq wanted me to post what the planned route is right now to clear up any confusion about what you have to do, so here goes.
Day 1
Get the PET and go to school.
Talk to Dex to make the tutorial start.
Manipulate 3 Cannons for the third tutorial. I know it can be done, we just need to figure out good timing for it.
Go home and jack into Lan's computer.
Talk to Glyde, talk to the lost program, bump into the door to sector 2, talk to Glyde again in Yai's computer and receive SpreaderGun I.
While you're doing all that, you could collect 2000z from random mystery data and buy a PowerUp now, depending on how useful a level 2 attack is in the next two dungeons.
Jack out, talk to Mom, jack into the oven.
You fight 1 Mettool here no matter what, so get the MetGuard G for GutsShoot from it. (ShockWave can be found as an item pickup to fill your library later.)
Get the IceBlock, which will make you have to get and use the WaterGun.
Fight FireMan with 4 swords.
Go to bed.
Day 2
Run all the way to the last door of the school.
Talk to every student once to make the class/attack start.
Talk to Dex. (GutsMan has to fail before MegaMan can try.)
Talk to Mayl and receive Roll R. Yai forces you to do this before you can jack in.
Jack in and journey through the school network, unlocking some doors as Lan with predefined answers, and others with numbers based on the frame count.
One door is optional to open; beyond it is another HPMemory if you find it's worth the time.
MegaMan gets zapped, so go to the corner desk of the AV room to free him. Also get the RepairPanelReturn A on the teacher's desk, because it's right there!
The last door makes you go free Mari for an ID card. Get the HPMemory while you're doing that.
After you use the ID, entering the last password makes you fight NumberMan.
You get warped back to 5A, so run all the way out of the school and to Mayl's house.
Jack into the piano and collect the Recovery-50 L, but not @Mayl.
Visit the Metroline station, talk to the worker in the corner, and ask "What caused it?"
Go fight Dex's upgraded GutsMan with 5 swords to receive /Dex and GutsMan G.
You could also jack in to get @Dex from the computer or get a CrossGun K and fight for a HighCannon G in the GameCube if they turn out to save time. (My tests show that the @Dex shortcut is about 3 seconds slower, actually, but I'd like someone else to try to confirm it.)
Jack into Lan's computer again and go toward StoneMan. If you haven't already, fight for DashAttack G. If you're using @Dex, bookmark that along the way too.
You probably won't be able to get all 4 random crystals to appear in the closest places to your path in sector 2, though. I would focus on getting the 2 1000 zennies in sector 1 again so you can buy a second PowerUp and do 3 per shot.
Oh, and fight a Swordy for a LongSword on the way to StoneMan if you want to form Beta-Sword or Sigma-Sword sometime.
After beating StoneMan with GutsShoot and whatever else you have, jack out and run to the Metroline.
Go to Government Complex, and grab a ticket to ACDC Town on the way outside, since I found it was a little faster.
The TV has one of the Escapes you need for that KnightSword trade, and the SciLab vending machine has 5000z if you have time for an extra jack-in.
Talk to the receptionist in the SciLab lobby to be able to use the elevator.
Jack into the computer and talk to the program.
Grab @Dad here, not because it's necessary, but because it sets up that great shortcut I thought up.
Run all the way back home, and Dad will send an e-mail with an HPMemory and a PowerUp. You have to open this e-mail before you can go to bed, so get @Mayl from the previous e-mail and CrossGun C from that old one (if you need more chips to trade) at the same time.
Now go to bed.
Day 3
Run to school again--this time you can use the first door to 5A.
Talk to Yai to make class begin and end.
This is the point when you can fight GutsMan's final form for more GutsMan or GutsPunch chips. This is also when the chip shop opens and you can do the old-man trades. The game really starts to open up now! (However, the last Escape you need isn't until the DenTown mission, so that's where the chip trader could come in handy.)
Go to the Government Complex again and get through the Chaud scene.
Go to Dr. Hikari's office and snip the ID.
Go up to the WaterWorks control room, grab the HPMemory, and talk to Dr. Froid (his control panel might be worth jacking into as well), then go down and to Dr. Hikari's office again.
Now go back to the WaterWorks and jack into the water cooler.
This would be another place to fight for AquaTower G or HiCannon G, but I haven't tested this far yet, so now I'm continuing based on some online guides and what I can remember having to do.
The water net is split into two branches, with one being inaccessible because of a broken handle. So take the first branch and end up fighting two of those ice-making polar bears (couldn't find the virus names for this game). Electric attacks would come in handy if you could find any, or you could just use Beta-Sword.
Now you'll automatically go back to ACDC Town and find that the school fountain water is tainted. I think you have to go back to the Metroline station, only to receive an e-mail that finally lets you open the car, but I have to double-check this.
Tory Froid gives you the Handle when you free him, so go all the way back to that water cooler and take the other path, grabbing the HPMemory nearby.
There's also a PowerUp right along the way, but it's hard to see. There's a sequence break in that area where you can skip turning on the first faucet by sliding just past two holes on either side of you, but the PowerUp is on the way to the second faucet, so no problem there.
Fight IceMan with ElecSword or whatever.
And then the day just ends with a bunch of cutscenes? Yeah, I think so.
Day 4
This time you start out as MegaMan in Lan's computer. Use your e-mail to accept Mayl's invitation, then take the response into Mayl's computer using @Mayl because her house is locked now. Once again, you could luck-manipulate a random item right on the path there.
You have to enter and exit the Metroline station once to start the scene that sends Mayl on her way to DenTown, despite MegaMan admonishing you for checking inside the station if you hit L there.
Once in Dentown, there's a couple more things to do before the big emergency mission. You could get the PowerUp from the summer school blackboard now, but at this point it's a detour, whereas later you'll be forced to visit there.
Open Mayl's message to receive RollV2 R and set up the meeting place.
Talk to Miyu once, so they "know" where to find antiques.
You should fight SkullMan now, since you're forced to talk to Miyu, and /Miyu is required to reach the Undernet. However, you could put off the battle until you come back to this town later, which I think would let you fight a more powerful SkullMan for a battle chip. Haven't really tested yet.
Once you've read that e-mail that had Roll2 and talked to Miyu, standing at the bus stop of Block 1 will begin the traffic accident sequence. I recall there's one more e-mail you're forced to read, either before or after you jack-in to the first light, I'm not sure, but it'll be obvious anyway.
Talk to the three people trying to buy the WWW program, then to Maddy, and then that starts the big chase around town where you jack into three more regular lights and then a round-the-block light.
You'll get to revisit the antique shop during this mission, but not the summer school, sorry.
Maybe win a DynaWave S in the color dungeons? It would go well with all those swords you start with.
At the end you fight ColorMan with GutsShoot and AquaTower or whatever. Then some more cutscenes...
Day 5
I recall this day starts you off in the park. Anyway, go tell Mom about the party.
Before you go to the Government Complex, visit Yai for 10000 zenny! That's got to be one of the quickest sources of money in the game.
If you talked to Mom, then Chaud will be at the SciLab. If you talk to him, then nothing interesting will happen, and MegaMan will suggest talking to everyone again. But actually, you just need to talk to the one guy standing right outside that TV lounge area, who tells you about the restaurant and power plant. Then when you go back to the middle of the lounge, the parents will arrive and you'll get to go to the restaurant. If you talk to that guy first, then when you talk to Chaud, Dad will appear immediately after... so do that.
In the restaurant, you need to talk to every single person once to start the next scene. This includes Lan's dad, who has another skippable custscene, but not people outside the restaurant, or inanimate objects.
Go down the dust chute.
Talk to the person outside the control room door, then talk to the person outside the generator room door, and this will make the first one open the control room door offscreen.
Jack in and do the power planet net, blah blah... Batteries are always used in the same location every game, so you can still use maps to spoil the solutions.
Fight ElecMan, but he'll heal whenever his HP reaches 550, so make him heal 3 times with 3 MiniBombs or whatever to end the battle and get Lan to turn the power off.
Fight ElecMan for real now.
Fight ProtoMan. Another boss that can be finished off with only GutsShoot! Since I don't think you get a chance to arrange your folder again between ElecMan and ProtoMan, Kirkq recommends picking a wholly different set of chips for the other fight, so you can set up some chips to fit into the first random arrangement the game picks, then set up the others to fit into the random arrangement that'll be chosen by the time the second fight starts. Sounds tricky, but doable.
Then I think all you have to do is talk to Mom, and you go home.
Day 6
You're looking for Chaud now, although you don't have to read the e-mail that tells you so in order to start this quest.
You do have to talk to the guy at the SciLab who says that Chaud went to DenTown. If you go to DenTown before you talk to that guy, Chaud won't be there.
Talk to Chaud in Central DenTown, and if you want, make a detour for SkullManV3. Now you know you need to find an ex-WWW-member.
That's Higsby, so go to his shop and talk to him behind the counter to get his HigsMemo. There are 3 other memos to find, but Lan doesn't know that yet, so you can't get them yet.
Log onto the Internet one more time, from Lan's computer or from Dex's computer if that route works out.
Get a few HPMemories from the shop if you need them to reach the 30-level goal.
Now you're going all the way to sector 5, collecting any random items that contain battle chips you don't already have for your library, or extra money if you still need that. In sector 2, take the opposite path from last time to use /Miyu and enter sector 4.
At the entrance to sector 5, you'll fight 2 Hardheads and 1 of those metal shield things, I think I read they were called Froshello somewhere or something like that, or maybe I just dreamed it. Why'd they wait 'til the second game to display the enemy names, anyway? Er, so yeah, that's two enemies in opposite corners with 90 HP that are only vulnerable when they're spitting cannonballs (Howitzers?), and one in the middle with 250 HP with a shield in front that only raises for a little while when you do a lot of damage to it, it's probably 100 or so, so figure out a combination of chips that will make short work of all of them and don't lose your footing. This might call for a level 3 Navi chip.
Now you'll get an e-mail from Higsby explaining the other three memos. You need to read it sometime, but don't jack out yet! Continue to the end of sector 5, then go through the one-way door into sector 9, then down into sector 3, where you can bookmark @Dad.
You could also fight StoneMan and visit the shop in sector 3. You'll probably want the WoodArmor just to raise yourself 6 levels, and StoneMan MIGHT come in handy because even the first-level chip can do 300 damage, but it is very slow.
Now make sure you have 60 chips in your library. If you don't, I guess that's one last stop at Higsby's, but let's try to plan ahead and minimize the number of side-trips to there.
Go back to the SciLab. Talk to the guy who wanders around going "Hmm..." for the first memo.
Now go to DenTown's summer school to get Yuri's memo. She's the one who checks to see that you've gotten 60 kinds of chips. There's a Barrier in the locker you can grab fast, so if you didn't have time to stop here earlier, then that may end up being your 60th chip.
Also, there's a PowerUp in the blackboard, so that's probably worth the jack-in time, too.
Now you can go back to ACDC Town and talk to the old man now standing in front of the empty house. No, you don't have to talk to the old men in the other towns; all they do is tell you that you've got the wrong guy. And the other old men in ACDC Town won't tell you anything new, because characters in trading sequences never comment on the main story.
If you got all the other memos and MegaMan is at level 30 or higher, the old man will give you Pa'sMemo. So if you have some extra PowerUps sitting around, make sure to equip them so they actually raise your level. (In general, try to combine trips to the Folder, E-Mail, and MegaMan's Status so you save a little time opening the menu, though it's not a huge deal if you can't.)
Now I recommend you go back to Dr. Hikari's office at the SciLab and jack into his computer.
This will allow you to start out at sector 3, where you can travel back to sector 9, then back to sector 5 through the now-two-way door, which puts you right at the entrance to sector 6!
Continue on to sector 8. At this point, you don't need to fill your library anymore, so only pick up things that actually help you from now on.
Fight BombMan. The guide says he's Fire-elemented, so AquaTower might come in handy again, though he loves to hide behind his bombs.
Jack out and talk to Dr. Hikari, who will be standing right there if you jacked in from his office computer. I noticed that at this point, ProtoMan and SharkMan are now powered up to their final levels, if that makes any difference to anyone. Now you can finally go home to bed.
Day 7
Leave your house, go to Higsby's, and you should find the WWW pass on the counter.
I think you talk to the Metroline worker in the back to find out you're looking for a secret subway line.
Then you find it in the school statue, but you find out you have to get the pass updated.
So you go to Dr. Hikari again, and you can finally get to the secret mountain fortress.
Should be pretty obvious from there on, except you have to check the Wily picture twice before you can jack in.
Next boss is MagicMan. Uh, luck-manipulate for easy enemies or something?
Then some cutscenes, spoilers, blah blah blah, and a short dungeon later, you get the final boss, LifeVirus. He has 1000 HP as well as a 100 aura that you can either spend a high-powered chip to break early, or you can wait for him to drop the aura on his own when he attacks, but you wouldn't have as much time to counterattack. I don't know what strategy might end the battle in one turn, but I did calculate that with maximum attack and speed, the Mega Buster could do 72 points of damage per second! Well, I'll try to find out how Hub.bat affects lower values too.
And then the first half of the ending is all skippable with Start. Our viewers aren't going to see very much story, you realize? It'll look like Lan has the power to blink and make people vanish. Oh well.
