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The Story Mode is a series of events that, designed by Sam, happen differently from the Pokemon franchise.
It is a the main story taking place in Johto. Unlike in PTD 1, the character can be moved around using arrow keys. There are wild pokemons and NPCs on different areas which the main character can interact. Tower Defense mode or dialogues would then follow.
In Tower Defense mode, very much like in PTD 1, pokemons can be placed on, removed from, moved among specified squares in a location. By using different moves, different objectives can be achieved. These objectives include killing incoming pokemons from getting resources at the end, or just wild encounter.
The following describes the major events that happen:
Afterwards, three shadow starters appeared in front of you. You need to fight them with three normal starters in your team.
Waking up from the dream, you remembered you can walk with arrow keys. Downstairs, your mum reminded you to get one starter from Professor after finishing your breakfast.
New Bark Town
One neighbour congratulated you in choosing a new starter as your pokemon. You then went to Professor's Lab. Professor greeted you inside and asked you to choose one of the starters (Chikorita, Cyndaquil, Totodile).
When you release it from PokeBall, the pokemon cries and runs away from you. You finally found your pokemon in the passageway northwest of the town. There, you saw the three starters pokemons were confronted by shadow pokemons. You used your chosen starter pokemon to kill the shadow pokemons before they get the other two starters away.
Professor knew what happened and summoned you back to his lab after reporting to the authorities about the roaming of shadow pokemons.
A mysterious voice was heard once you stepped the lab again, which tells you to go to the southeast part of the town "alone". There, a redheaded guy asked you to fight him. Strangely, he owns a starter which is effective against you, plus a Sentret.
After the fight, the professor summons you again to give you a newly-developed PokeBall, which allows you to catch weakened pokemons with infinite number of use.
You saw a guard caught the mysterious guy you have just fought. You heard his name is... Silver.
This route was a large area. You went deeper and you saw a girl, Zai. She asked you for your help in defending her Oran Berries for her. As you fight, you found a catchable shadow pokemon.
To the north, there was a rest station, blocked by a guard. Since you cannt get past, you continued to walk west.
- Main article: Cherrygrove City
When you talked to the guard, Professor, Silver, and Zai came and all of you entered Cherrygrove City. There, you saw Gary persuading Zapdos not to attack wild lives.
You and Silver decided to help with your pokemons by knocking down the rattled pokemons while evading Zapdos's attack. After all this, Ash appeared and his Lugia calmed the legendary birds with telepathy. Giovanni appeared from nowhere and captured Lugia with his new invention, Mewthree.
You can talk to grandpa in the south for a pair of running shoes.
Walking through Route 30, you saw many new pokemons that you were interested in getting them. You also see a professor standing in front of a cave, claiming he has finished installing the lights inside the cave. Inside, you can see some geodude and zubat. He is puzzled since you look familiar to him.
At the end, you saw a guard blocking your way again. This time, a blue-headed guy claimed himself the gym leader of the city ahead. You then challenged him and you two fought in a clear area in the forest. The guys was a fanatic collector of pidgey that more and more came in as battle proceeded. The guy's pidgeotto also wings up strong gusts of wind that caused you high damage continuously. You receive TM Roost from the guy.
Seeing you beating the gym leader, the guard was terrified and let you through.
- Main article: Violet City
An uneasy monk came to you and asked your help in gaining control of the Sprout Tower in the north. Inside, you saw shadow Bellsprouts. The alpha Bellsprout in the center occasionally summons vine whip that traps your pokemon in place. Then the fellow Bellsprouts would fire razor leaves that hit your pokemons for a small damage. The monk inside the Tower thanked you for your effort and referred you to Elder Li in the city for help.
Giovanni appeared again and this time, he shadow captured all citizens into Mewthree's Shadow realm (Shadow Catpure). Inside, everyone was angry. Lugia there speaks of causing a turbo of air current to break the shadow realm. To save the rest, you had no choice but to fight against Lugia. Zai volunteered in healing your pokemon at a corner. Lugia summons whirlwinds to any one pokemons around it. It also wing a strong tornado that kept hitting your pokemon for damage if not removed in time.
You finally returned to reality. If you talked to the blue-headed guy, you will accept your second challenge as a gym leader. This time, two Pidgeottos appear at the same time.
Route 32 (North)
Ruins of Alph
- Main article: Ruins of Alph
You thought the Crobat was not trouble at all and decided to get back to him for more experience. In the ruins, you found the two entrances led to the same area and some uowns inside. Investigation leads you to know that the uowns were fighting for the fossils. Not knowing more information, you defended the fossils. You asked for Ash's help outside the ruins, he insisted that you have missed something.
Ash and Gary came inside the ruins. Ash told you for the time being when they investigated more, you should check out more Route 32.
Route 32 (Central)
The other guard have stepped aside to let you pass. You found more pokemon you liked on the way. At the end, you saw a fisherman that have caught a large amount of different pokemons in different weeks. Each time you were asked to defend the rare candies at the right side. At first, the fisherman gave you an Old rod. When you have defended for the three types of pokemons the fisherman caught (Tentacool, Magikarp, Qwilfish), the fisherman was surprised and awarded you the Good rod.
When you proceeded further down, you witnessed Mewthree captured the fisherman and Silver plus Zai coming to you. You summoned your pokemon to protect you from being caught.
- Main article: Past World
A whole new world
After defeat, you could not see Mewthree but Celebi arrived at you, saying you have just brought down one clone of Mewthree. Celebi brought you back a few minutes before Mewthree appeared to talk these words to you. Putting you as a hope to the world, Celebi requested you to get stronger to fight the Elite Four and Giovanni, just like Gold did in the past. Celebi teleported you to the past when Gold first started his journey. You arrived at your hometown but no one could recognise you, even your mum.
You cannot see Zai anywhere. Instead, you can see trainers that challenges you when you are near them. There is no guard to block the entrance to the north. The wild pokemons are just the same as in present.
There is a grandma that remembered how Bellossom was and gives you flowers. There is a trainer from the twin too. On the coast, the fisherman teaches you the time to fish Corsola. You are surprised to see all PokeMarts opens in the past time. You had good time shopping for items.
There are more trainers on the way, both on the left way and right way.
In front of the cave, you cannot see the professor as in present. The blue-headed guy is not here too.
There are some trainers in the city, inside the school, the tower, and the gym. Inside the gym, the blue-headed guy cannot recognise you and challenges you indoor. After you defeated him, he gave Zephyr badge. The fat guys trading his Onix is not here anymore. Instead, he guarded the northwest entrance. Not seeing three gym badges, he does not let you pass.
Trainers are still everywhere. Other than this, nothing else has changed. Route 32 (south) is a long way and a good place of nice view. You feel difficult to choose either the pawn path or promenade path. But you can see there is a fisherman trainer far in the promenade path. No matter which path you choose, you would arrive at PC and a huge cave.
This is a large cave indeed with many floors. The north ladder leads you down to B1 with a trainer and large pond you cannot pass. Deep in the cave, there are many hiker trainers, and many wild pokemons as well. You feel a bit annoyed to getting past them. Also, you see wild Onixs that you traded for... WTH! Finally, you can leave the cave at the southeast corner.
On the way to the town, you see an intersting well. The guy standing next to the entrance shows off his Slowking by challenging you. Inside the cave, you see rarely Slowpoke. Perhaps the Slowking is evolved from Slowpoke? More rarely, you see some Slowpokes are holding King's Rock. What is the Rock used for? The Pokeball master inside city complains about the loss of berry trees. This caused him idle for long. The way is blocked by a hiker. You have no choice but to go to gym. Inside the gym, you would rather call that "forest", there are strong bug trainers. The trainers are not a problem at all. When you challenge the gym leader, you feel some magic force that widens the gym space. The trees are gone too! Anyway, you beat the Ariados that can summon swamps of Spinaraks by binding pokemons in spider webs. The fast moving Scyther is little hard to hit too! That Metapod is a bit trouble if you let it live for long. Anyway, you beat the purple-headed guy and get the badge. She gives you the TM U-Turn. The hiker is now gone.
Just when you enter this huge forest, the child asks you for help. He needs to find his Farfetch'd. In return, he promises to give you HM that can "cut". You find that the forest is very much exploited with little trees left. You easily find the Farfetch'd at the northeast corner. Talking to it will make it furious and fights you. Seeing you are a trustworthy person, it says it wants home. Telling the child you have defeated his Farfetch'd would impress him and hands you Cut HM for a return. Strangely the Farfetch'd does not go and could fight you with more friends. Although you feel tired late at night, you cannot believe the pokemons are totally different in the nighttime.
- Main article: Goldenrod City
They say Goldenrod City is kidnapped by Team Rocket. Oh gosh, it is true. The PC, north station, gym are all closed. No wonder why the lady (red-headed this time?) runs on the main road for help. She at first looks down on you having just 2 badges. On second thought, she had no choice and first challenges you as a gym leader. The Miltank would do Rollout along a path for great damage. That milk cow has high defense and HP. You are surprised to find the Clefairys cannot be harm by traps and status problems. The lady hands you Plain Badge and TM Attract. (Has she used Attract on me? I find her much beautiful after battle...) She tells a plan to defeat the Team Rocket.
- Rocket trainer southeast of PokeMart
Once inside the bike shop owner would thank for you help and give you bike for faster travel.
- Rocket trainer north of PC
Once inside, the Game Corner owner would allow you to play Voltflip for game coins.
On the main road, you would now see four Team Rocket members confronting that beatiful lady. Of course I need to stand for her! A stupid guy runs all over the rectangle battlefield while the others standing by side and throws in pokemons. After defeating those mobs, Giovanni appears as the leader and blames his followers for robbing the city. You gain the impression Giovanni is nice. Suddenly, Mewthree appears and revenges on Giovanni. Mewthree claims it also time-travelled just like you do. Then it suffers from pain and explodes into Shadow Lugia. Giovanni admires the transformed Mewthree and follows it.
You found that this is a shortcut going back to Violet City and Ruins of Alph. That way, you would not need to run all the way long. To the north, there is a strange, brown "tree". The Pokedex tells you it is a Pokemon called Sudowoodo. You decided to clear the path. During the battle, you found that "tree" has very high HP. When you defeated it, the "tree" does not "grow back". So, you thought you should have caught that Sudowoodo in time.
All the way through the Routes, you see shadow pokemons roaming in the city again. The Kimono girls are on trip, the Ho-oh tower is blocked. Only PC, PokeMart remain their service. Wait, the guy wearing purple headband seems to be the gym leader? This gym plays good on the four directions. Each time the Gengar boss has down 1/4 health, it will summon its shadows to heal itself. If the shadows are not defeated in time, the boss get healed. As a reward, that Morty will give you Fog Badge plus TM Shadow Claw. Now perhaps the guys blocking the west and east way would let me pass.
- Main article: Olivine City
Just when you enter the city, you hear some noise. Then you see the wound Ho-oh lying on ground. The Shadow Lugia ("Mewthree") is under uncontrollable rage. The legendary Ho-oh appears and mistakes it as its friend Lugia. Ho-oh tries to defeat Mewthree but at the final confront, Mewthree overwhelms Ho-oh, upsetting Ho-oh's last hope of saving world...
In the town center, there are many citizens, so as two outstanding people: a muscle man and a sweet girl. The girl, Jasmine, called the muscle man to come to see if the Ho-oh is real. Suddenly Ho-oh speaks of you, as the "Chosen one" long time ago, having a pure heart to fight. These two people then train you as the gym leaders.
The two gym leaders stand on left and right. Sometimes they will release pokemons at the same time. The pokemons are moving fast though, some even put on Protect. It is a bit hard to defend the candies at the end. With some tactics, they are not so difficult.
Onwards, the muscle guy gives you Storm Bagdge plus Focus Punch TM. You receive Mineral Badge and the TM Iron Tail. Silver suddenly appears at the city entrance to give you HM Surf. Now I can explore more areas!
There are two paths in front of you: cave, or waters.
In the caves, you find several level 50-60 wild pokemons. Thanks to those, your pokemons have more levels.
When you surf through the waters, you find a cavern in the middle. Marills only appear there at night.
The grandma do not let you pass the road to the right. You have to fight the Ice Gym leader. He stands at the center and promtly accepts your challenge.
Go up through the north path, you see a new pokemon, Girafarig. Again, all pokemons would come into battlefield if you bump into any.
Further north, there are Gyarados in the lake. Across the lake, you see a botanic house. Sam awaits inside the house, claiming this is his vacation house. You are so surprised to see his collection of Outer space pokemons: strong and a huge team.
You now found that when you bump into any pokemon, all kinds of pokemons would rush towards you in battlefield. The environment of the battlefield has a different layout too. Is it some sort of magical power?
All kinds of pokemons would appear in the battlefield. Even though you cannot see Sneasels in the cave, surprisingly they will randomly battle you.
All citizens are in the same orange uniform. Although feeling strange, you ask one of them about the gym. He said the gym is closed, but the gym leader is in the Dragon's Den that you might have a look there.