Outskirt Stand:

After beating the Realgam Tower and therefore restarting the game, you end up in the bar of the Outskirt Stand from the start of the game.
If you didn’t manage to catch a Pokémon in the Realgam Tower, don’t worry, you can go back there.
From now on, pay close attention to the mails you are going to receive on your P*DA, because they are going to arrive in great numbers.

In fact, a mail from Nett arrives right away: it gives you hints about the Shadow Pokémon spotted across the country and catalogued by Team Cipher.
From now on, you can complete your list of 50 Pokémon, precisely. (out of 53 ; Togetic, Ho-Oh and Celebi are the 3 others left).

Togetic.

As you leave the bar, a mail from Nett tells you that a Shadow Pokémon has just been spotted in … Pyrite Town.

Pyrite Town:

Head straight to Duking’s place and open the wardrobe, where you will find a secret passage behind it. The young girl sitting at the desk, Lenn, gives you more precise hints than Nett about the Shadow Pokémon. She advises you to go and pay a visit to our little Eagun the thug (well, well … what a coincidence! Always where he shouldn’t be), the green-haired man standing at the entrance of the town. As usual, a little battle is in order.

The Colosseum in Pyrite Town
Trainer:
Eagun the Thug
Shiftry (Dark/Grass, Level 56), Granbull (Normal, Level 56), Gardevoir (Psychic, Level 57) and Machoke (Fighting, Level 57)

Once defeated, Eagun explains that the Trainer who owns a Shadow Pokémon talked about the Team Snagem hideout. Ta-da! A new location appears on the right of your map. By the way, the Shadow Pokémon in question is none other than one of the 3 Gold/Silver starters and, as it happens, one of those you did NOT choose in Phenac City at the beginning of the game. If you wish, you can also go back to the Pyrite mines, where you can find Pokémon you didn’t manage to Snag.

Team Snagem Hideout:

Pyrite Town

You receive a mail from Lenn as you enter the building. She gives you the name of the Trainer (Rosso, Bluno or Verde). Note that the one you chose to face in Phenac City at the beginning of the game will stay stuck at the Game Corner in the Realgam Tower until you obtain his Shadow Pokémon, in case you haven’t already done so. In the hideout, one of his henchmen is waiting for you instead.

Most of the battles in there are completely optional. Only one is essential for you: the one where you can catch Quilava, Croconaw or Bayleef. Either way, you will have plenty of items to pick up from the ground (a Max Elixir at the entrance, for example).
Anyway, the entrance is a dead end. To get in, you have to go back and enter through the first door on the right, into the room where you will find a PC to save. As you move forward, you are approached by a member of Team Cipher. These individuals will always be members of Team Cipher who own or used to own Shadow Pokémon. Basically, everyone you met without being able to catch their Pokémon (except those from the Shadow Pokémon Lab) is in here.
A few examples?

Bayleef.
Trainer:
Cipher Peon WILD
Ninjask (Bug/Flying, level 55), Beautifly (Bug/Flying, level 54), Forretress (Bug/Steel level 51), Masquerain (Bug, Level 52), SHADOW Yanma (Bug/Flying, level 33)


Trainer:
Cipher Peon GINY
Jumpluff (Grass/Flying, level 53), Vileplume (Grass/Poison, level 51), SHADOW Sunflora (Grass, level 45)

As you go on, Nett sends you information to complete your list of Shadow Pokémon. (he’s useful, that little guy! ;)) In the meantime, keep defeating Trainers until you reach our brave Rosso/Bluno/Verde … the moment of deliverance is finally yours!

Trainer:
Cipher Peon Rosso/Bluno/Verde
Muk (Poison, Level 55), Grumpig (Psychic, Level 54), Breloom (Grass/Fighting, Level 53), SHADOW Quilava/Croconaw/Bayleef (Fire/Water/Grass, level 30)

Now, you will have to change town 3 times to continue your adventure …

Under:

You receive a mail from Nett …

Pyrite Town:

And here you receive a mail from Lenn …
She tells you to go and see TEUG in Under. Hurry there!

The underground city of Under

Under:

TEUG is in the south, up the stairs, facing the old shop. He is dressed in purple with a yellow scarf. Anyway, he battles you, and it is actually rather easy if you have a Grass or Electric Pokémon …

Trainer:
Rogue TEUG
Wailord (Water, Level 56), and … Wailord (Water, Level 56)

Once he is defeated, he reveals the identity of the Shadow Pokémon (Quilava, Croconaw or Bayleef) and its Trainer (Bluno, Rosso or Verde …). It depends on the 2 other Trainers you have faced, but note that it is the last one from whom you can Snag a Gold or Silver starter.
Go back to Pyrite Town.

Quilava.

Pyrite Town:

Another trip for next to nothing: you receive a mail telling you that your target is located … … (I can hear some "where? where?!" in the back …) … … … at the Research Lab!
What are you waiting for? Rush over there!

Research Lab:

Take the shortest path to the former office of our dear and fallen Admin Ein. On the way, several Trainers you have already met battle you.

Trainer:
Cipher Peon Therma
Sharpedo (Water/Dark, level 56), Nuzleaf (Grass/Dark, level 57), Houndour (Fire/Dark, level 56) and SHADOW Murkrow (Dark/Flying, level 45)


Trainer:
Cipher Peon Mara
Pupitar (Ground/Rock, level 56), Swablu (Normal/Flying, level 58), Golbat (Poison/Flying, level 56), Mawile (Steel, level 57), SHADOW Forretress (Bug/Steel, level 43).


Trainer:
Cipher Peon Lesar
Rhydon (Ground/Rock, level 57), Grovyle (Grass, level 56), Masquerain (Bug/Flying, level 57) OR SHADOW Ariados (Poison/Bug, level 43).


Trainer:
Cipher Peon Fia
Linoone (Normal, Level 42), Vigoroth (Normal, level 44), Delcatty (Normal, level 43) OR SHADOW Granbull (Normal, level 43).


Trainer:
Cipher Peon Izuna
Swellow (Normal/Flying, level 58), Kadabra (Psychic, level 57), Kecleon (Normal, level 58), Quagsire (Water/Ground, level 58) OR SHADOW Vibrava (Ground/Dragon, level 43).

As soon as you set foot in Ein’s office, a Trainer jumps on you… Get ready to draw your Pokémon!

Trainer:
Cipher Peon Rosso/Bluno/Verde
Grumpig (Psychic, Level 62), Camerupt (Fire/Ground, Level 61), SHADOW Quilava/Croconaw/Bayleef (Fire/Water/Grass, level 30)

Now back in the open air, you receive a mail from Nett. He tells you that you can receive photos by mail and, above all … that two Shadow Pokémon have been spotted: Ursaring and Smeargle. To reach them, head to the Team Snagem hideout!

Smeargle.

Team Snagem Hideout:

In this hideout, you can snag the following Shadow Pokémon:
– Hitmontop (Fighting, level 38)
– Ledian (Bug/Flying, level 40)

Ledian.

And at the end you meet two Trainers: Zabb and Midzano.
Here are their details:

Trainer:
Team Snagem Zabb
Smeargle (Normal, Lv. 50), Smeargle (Normal, Lv. 50), Smeargle (Normal, Lv. 50), SHADOW Smeargle (Normal, Lv. 45).

and …

Trainer:
Team Snagem Midzano
Marshtomp (Water/Ground, level 55), Shiftry (Grass/Dark level 50), Machop (Fighting, level 52), and SHADOW Ursaring (Normal, level 45).

Now go and heal up in the nearest town, and you receive many mails telling you that you must go back to the Team Snagem hideout to meet Gonzap again.
Be careful, he is very well hidden and you are at serious risk of not meeting him.
He is near his office, and you might think … that he was waiting for you.

Gonzap
Trainer:
Team Snagem Gonzap
Breloom (Fighting/Grass, level 64), Crawdaunt (Water/Dark, level 64), Armaldo (Bug/Rock, level 64), Granbull (Normal, level 64), Machamp (Fighting, level 64) and SHADOW Skarmory (Steel/Flying, level 47).

The boss, humiliated, walks away, leaving a shiny disc on the table. This disc takes you to the depths of Under, the basement of the basement, where it is darker than dark.

Under:

Go to the flying saucer and use the disc to lower the platform.
And you arrive in … the Under!

Under Colosseum:

Head to the wide corridor to open a gigantic door to the north… which leads you to the hall of an all-new Colosseum !

Of course you meet all the Team Cipher Admins again as bosses (from Miror B. to Ein, naturally), and once you have beaten the Colosseum 5 times, a mysterious Trainer, the king of the Under, arrives with the LAST (or almost … ;)) Shadow Pokémon of the game.

Miror B.

Each time you win, you pocket 20,000 Poké Dollars… as well as TMs:
First victory: TM12 (Taunt)
Second victory: TM48 (Skill Swap)
Third victory: TM44 (Rest)
Fourth victory: TM02 (Dragon Claw)

Save after your 4th victory and keep battling until you meet the king.

Trainer:
King of the Under
Girafarig (Normal/Psychic, level 68), Kingdra (Water/Dragon, level 70), Skarmory (Steel/Flying, level 66) Sableye (Ghost/Dark, level 69) and finally SHADOW Shuckle (Bug/Rock, level 45).

Make sure you have all the Shadow Pokémon and … the adventure continues.

Phenac City // Outskirt Stand:

Phenac City

Hit the road again and head, for example, to Phenac City … and … what a disaster! Your perfect lookalike is attacking the poor inhabitants of the Orre region. 🙁
Of course this ruins your reputation and everything you managed to save is ruined. (phew)
After a while, by dint of travelling and watching television, you locate the infamous fake hero.
Make sure you have a Snag Ball and rush into battle!

Trainer:
Fake hero Masq.
Armaldo (Bug/Rock, level 68), Gyarados (Water/Flying, level 68), Milotic (Water, level 68), Electrike (Electric, level 68), Houndoom (Fire/Dark, level 68) and FINALLY!!!… SHADOW Togetic (Normal/Flying)

Tip: Before Snagging poor little Togetic, get rid of ALL the colossi surrounding it. Keep a cool head, the little one is level 20, and a direct attack would ruin your chances forever of catching little Togetic and therefore … of obtaining Ho-Oh and finishing the game.
So wait for the little one to hurt itself by striking with its Shadow moves and keep your own Pokémon waiting. When Togetic’s bar reaches yellow or red, put it to sleep and then throw your Ball.

Congratulations! You have just caught the last Shadow Pokémon of the game! Now, you have to purify them all (yes, it’s looooooooong…) and take on Mt. Battle in Battle Mode to grab the last secret the game holds: Ho-Oh …
But that is no longer the role of this walkthrough. 😉

THE END!