Walkthrough

This walkthrough follows the main story of Pokémon Scientist from Pallet Town to the Indigo Plateau, and beyond. Each chapter covers a major stage of the adventure and links to detailed pages for every route, city, dungeon, and other important location you’ll visit. These pages include location-specific information such as wild Pokémon encounters and will continue to expand as the project develops.

Chapter 1 — Pallet Town

Chapter 1 Spoilers

Name your character and your rival.

Choose your starter Pokémon.

Receive the Pokédex.

Use the PHONE to withdraw the Potion from your PC.

Each starter has a unique strategy for defeating the rival’s Porygon.

• Grimer

Use Harden early to withstand Tri Attack. This is generally the most difficult opening battle, so don’t be discouraged if it takes a few attempts.

• Magnemite

Open with Thunder Wave, then use Screech three times before attacking with Tackle. Avoid SonicBoom, as Porygon may use Conversion to become Electric-type. Remember that Screech only lowers Defense, so it will not increase SonicBoom’s damage.

• Koffing

Use Poison Gas before Porygon can use Conversion, then stack Smokescreen until its accuracy is heavily reduced. Once Porygon is struggling to land attacks, finish it with Tackle.

Oak’s aide gives you five Poké Balls. The female aide also hints at the recently dismissed laboratory assistant, an optional side quest that can be completed shortly.

Travel north through Route 1 to Viridian City. Wild Pidgey frequently use Whirlwind, preventing you from gaining experience, so it is usually more efficient to run from these encounters.

Chapter 2 — Viridian City

Chapter 2 Spoilers

Collect Oak’s Parcel from the Viridian Mart.

Although the parcel is actually a Master Ball, using it has lasting story consequences. Professor Oak will question you about what happened. You can confess or lie, and each choice has unique dialogue.

Purchase a Poké Doll from the Viridian Mart. It is expensive, but bringing it to the dismissed laboratory aide in Pallet Town rewards you with a Bulbasaur, making it one of the most valuable early-game purchases.

Visit Route 22 and consider catching either Mankey or Nidoran♂. Both provide early access to Fighting-type attacks that remain useful throughout the game.

Challenge your rival on Route 22. A team containing Bulbasaur and Mankey makes this battle much easier. Keep in mind that Leech Seed will fail against Grass-type Pokémon such as Tangela. Training to around Level 10–11 before attempting the battle is recommended.

Before Viridian Forest, you may notice that two bushes have been removed from the passageway to the Viridian Gate. Talk to Oak’s aide at this gate to earn HM01 (Flash). Flash has been repurposed for Scientist, lowering accuracy of the target by two stages instead of one, and furthermore, all of the Pokémon that are obtainable in this first leg of the story can now learn Flash. Flash works in more locations, but simply serves a cosmetic purpose, to restore the original palette of the forest and cave maps (which have been made dim instead of dark) rather than to illuminate them completely.

Continue through Viridian Forest. There are only three mandatory trainer battles, but the forest is an excellent place to catch the rare Venonat or Pikachu.

Chapter 3 — Pewter City

Chapter 3 Spoilers

Defeating Brock is not required immediately. If your team is struggling, you can postpone the Gym battle and return later with additional experience.

Route 3 provides several trainer battles that are ideal for training before entering Mt. Moon.

Brock awards TM18 (Counter) instead of TM34 (Bide).

Bulbasaur can defeat Brock almost single-handedly with Vine Whip or Razor Leaf.

An alternative strategy is to purchase a Fresh Water and give it to the Cooltrainer near the entrance to Mt. Moon. He rewards you with a Squirtle, which can be trained inside Mt. Moon before returning to challenge Brock.

Mt. Moon contains numerous useful Pokémon and items. Jynx can be caught here and later traded for Lickitung. Defeat the Super Nerd at the end of the cave to claim one of the two Fossils, which can be revived later in the game.

Chapter 4 — Cerulean City

Chapter 4 Spoilers

Your rival awaits immediately north of Cerulean City. By this point your team should be around Levels 18–22, making this a good opportunity to evaluate how your party is developing. His team has considerably more coverage than in the original games, so avoid relying too heavily on a single Pokémon. Defeating him grants access to Nugget Bridge and the routes beyond.

Nugget Bridge consists of five consecutive trainer battles followed by an encounter with a Team Rocket Grunt. Heal your team before challenging the Grunt, as he can be more dangerous than the trainers preceding him. Victory rewards you with a Nugget, which can be sold for ₽10,000 to help fund supplies before the next Gym.

Continue east along Route 25 to Bill’s cottage. After defeating the trainers along the cape, speak with Bill and assist him with his teleportation experiment. As in the original games, he rewards you with the S.S. Ticket, allowing you to board the S.S. Anne in Vermilion City.

Once Bill’s experiment has been resolved, the S.S. Ticket is yours. This marks the end of the Cerulean chapter and opens the route toward Vermilion City via Routes 5 and 6.

The Rocket Grunt at the house formerly guarded by a Police Officer rewards you with TM28 Dig after his defeat. Dig is a powerful early-game Ground-type attack and gives several Pokémon an effective answer to Electric- and Poison-types, making it one of the most useful TMs available at this stage of the game.

Misty’s team is considerably stronger than in the original games, but there are several excellent counters available by this point. Grass-types remain the safest option, while Electric-types can also perform well against much of her team. Defeating Misty earns the Cascade Badge and TM11 (Bubblebeam).

A trainer in the Cerulean City Pokémon Center offers a Charmander in exchange for a Butterfree, which can be caught previously in Viridian Forest or presently on Route 25. This is an excellent trade, but keep in mind that Charizard’s high experience growth means it may evolve quickly if you’re using the redesigned EXP.ALL. Because Charizard is obtained through a trade, it can begin disobeying your commands before earning additional Gym Badges.

The Day Care on Route 5 has been reworked. In addition to raising one of your own Pokémon, the attendant is secretly a Pokémon breeder who rewards you with a Level 5 Pokémon after every 1,024 steps you travel. Be sure to stop by periodically, as this provides a steady source of additional Pokémon throughout your adventure. However, given that stat EXP is nullified in Pokémon Scientist, the bred Pokémon won’t have higher stats if you train them from Level 5 compared to higher level Pokémon found in the wild.

With Bill’s experiment complete, the S.S. Ticket is yours. Before continuing to Vermilion City, take the Underground Path beneath Saffron City to reach Route 6. This passage bypasses Saffron, which remains inaccessible until later in the story.

Chapter 5 — Vermilion City

Chapter 5 Spoilers

Talk to the Chairman of the Pokémon Fan Club to receive HM02 (Fly). Once Fly has been obtained, fast travel becomes available for the remainder of your adventure, making exploration and backtracking significantly more convenient.

At this point you can fly to Fuchsia City, where you should continue east to the Route 15 Gate. On the second floor, one of Professor Oak’s aides rewards you with the redesigned EXP.ALL. Unlike the original version, EXP.ALL provides experience to your entire party without splitting experience between participants, making it one of the most valuable items in the game. From this point onward, training newly caught Pokémon becomes dramatically faster.

You can also visit the Safari Zone to catch some strong Pokémon and to obtain HM03 (Surf) from the Safari Zone Secret House. While you’re at it, grab the nearby Gold Teeth and return them to the Warden at the Warden’s House (just east of the Fuchsia City Pokémon Center) to obtain HM04 (Strength). While Surf has not been changed in this version, Strength is now the Fighting-type equivalent of Body Slam, complete with chance to inflict paralysis, and is a very potent move against Normal-type Pokémon.

Return to Vermilion City and present the S.S. Ticket at the harbor. The ship contains numerous optional trainers and items, providing an excellent opportunity to strengthen your team before the next Gym. It is worth exploring every cabin before continuing to the upper decks.

Your rival appears aboard the S.S. Anne before you can meet the ship’s captain. His team has grown considerably stronger since Cerulean City and includes several Pokémon capable of covering common weaknesses. Be sure to heal beforehand, as this is one of the more demanding rival battles in the early game.

After defeating your rival, visit the ship’s captain to receive HM01 Cut. Although HMs are no longer restricted by Gym Badges in Pokémon Scientist, Cut remains essential for accessing several optional areas and progressing through parts of the main story.

With Cut in hand, enter Vermilion Gym and challenge Lt. Surge for the Thunder Badge. Electric-types remain dangerous, but the redesigned type chart and expanded Pokémon availability offer many viable strategies. In particular, a Pokémon with Dig or a bug-type move such as Pin Missile can sweep the Electric-types in this Gym.

Chapter 6 — Celadon City

Chapter 6 Spoilers

Celadon City’s Radio Tower has replaced the original Game Freak offices and plays a central role in Pokémon Scientist’s story. Reports of strange activity inside have disrupted communications throughout Kanto, preventing access to Saffron City. Before challenging the Gym, investigate the upper floors of the building to uncover the source of the disturbance.

Approach the Radio Tower from the back entrance, and you will take a set of stairs that leads to the roof. At the top of the Radio Tower, confront the Team Rocket operative responsible for sabotaging the communications network. This Rocket has six Level 30 Magnetons, which can prove dangerous if you don’t have a solid Bug- or Ground-type offense. Although this is only a single battle, it marks an important turning point in the story. Once defeated, communications are restored, allowing the authorities to reopen access to Saffron City.

Celadon Department Store is one of the best places in Kanto to prepare for the remainder of the game. In addition to its extensive selection of items, it now offers several exclusive services unique to Pokémon Scientist. Be sure to visit the Tradeback NPC located inside the Department Store. This character allows Pokémon that normally require trading to evolve without using a second game, making it possible to complete your team entirely within a single playthrough. If you’ve been saving Pokémon such as Kadabra, Machoke, Graveler, or Haunter, this is an excellent opportunity to evolve them. Stock up on healing items while you’re here, as they will remain useful for the rest of your journey.

With the Radio Tower incident resolved and your preparations complete, challenge Erika for the Rainbow Badge. Her Gym specializes in Grass-type Pokémon, but her team has been redesigned and is more versatile than in the original games. Fire-, Flying-, Bug-, and Ice-type attacks all perform well. Defeating Erika grants the Rainbow Badge.

Although communications have been restored, Team Rocket’s influence extends far beyond the Radio Tower. Strange activity at the Celadon Game Corner leads to the discovery of the organization’s hidden headquarters beneath the city. Search the suspicious poster to reveal the concealed entrance and descend into the Rocket Hideout.

The Rocket Hideout is a multi-floor dungeon filled with Rocket Grunts, locked doors, and the familiar spinning floor panels. Bring a healthy supply of healing items, as there are numerous mandatory battles before reaching the deepest level. Exploring every room is worthwhile, as the hideout contains several useful items that can make the upcoming Gyms considerably easier.

At the lowest level of the hideout, you’ll face Giovanni, the leader of Team Rocket. His team is significantly stronger than in the original games. Ground-, Fighting-, and Water-type Pokémon perform well, but be prepared for broader move coverage than veterans of Pokémon Blue may expect.

Defeating Giovanni forces Team Rocket to abandon the hideout and rewards you with the Silph Scope. This item is required to identify the ghost haunting Pokémon Tower in Lavender Town and marks the beginning of the next major stage of the adventure. Before leaving Celadon, make sure you’ve completed any remaining business at the Department Store and challenged Erika, as your journey will soon take you back across Kanto. Make sure to pick up the Bike Voucher from the woman in the house behind the bush west of Celadon City (where HM02 was awarded in Blue). Flying to Cerulean City’s Bike Shop will award you with a bicycle that is twice as fast as running.

Chapter 7 — Lavender Town

Chapter 7 Spoilers

With Fly now available, Rock Tunnel is no longer a mandatory part of the adventure, but it remains well worth exploring. The cave contains numerous trainers, valuable items, and several uncommon wild Pokémon, making it an excellent place to gain experience before continuing to Lavender Town.

Upon reaching Lavender Town, make any necessary preparations before entering Pokémon Tower. Ensure you have the Silph Scope, as it is required to identify and battle the ghosts that haunt the upper floors. Stock up on healing items.

Your rival awaits on the second floor of Pokémon Tower. His team has continued to evolve and features a balanced selection of Pokémon capable of punishing unprepared teams. Heal before approaching him, as this battle serves as the first major obstacle inside the tower.

The third through sixth floors are occupied by Channelers possessed by restless spirits. With the Silph Scope, the ghosts reveal their true identities and can be defeated normally. The tower contains several useful items and opportunities to fully heal your party, making exploration worthwhile despite the large number of trainer battles.

The seventh floor has been occupied by Team Rocket, who have taken Mr. Fuji hostage. Defeat the Rocket Grunts guarding the summit and rescue Mr. Fuji to bring peace back to Pokémon Tower. After returning to his home in Lavender Town, Mr. Fuji rewards you with the Poké Flute, allowing you to awaken the sleeping Snorlax blocking Routes 12 and 16 and opening multiple new paths through Kanto.

Chapter 8 — Fuchsia City

Chapter 8 Spoilers

Before challenging Koga, make sure you have collected HM03 Surf from the Safari Zone and HM04 Strength from the Safari Zone Warden. Neither HM is locked behind Gym Badge requirements in Pokémon Scientist, making them immediately useful for exploring previously inaccessible areas. If you skipped either of them earlier, now is a good time to return and pick them up.

Koga’s Gym makes heavy use of Psychic-type Pokémon, despite being a Poison-type Gym, making Bug- and Ghost-type attacks particularly effective. Fire-types are also valuable for dealing with his remaining Poison-types, giving Pokémon such as Charizard an opportunity to shine. Build a balanced team rather than relying on a single type advantage, as Koga’s expanded movepools can punish overly specialized strategies. Defeating Koga earns the Soul Badge and prepares you for the battles awaiting in Saffron City.

Chapter 9 — Saffron City

Chapter 9 Spoilers

If Saffron City is still inaccessible, return to Celadon City and complete the Radio Tower storyline. Restoring communications allows the guards to verify your identity and reopen the city, granting access to both Silph Co. and Sabrina’s Gym.

Silph Co. has eleven floors connected by a network of teleporters, making it one of the largest dungeons in the game. While it is possible to rush directly to the end, thoroughly exploring the building rewards you with valuable items and opportunities to train. Be prepared for numerous mandatory battles against Team Rocket before reaching the upper floors.

Your rival confronts you partway through Silph Co. with one of his strongest teams yet. His Pokémon cover a wide range of types, making this an excellent test of your party before the battles that follow. Heal beforehand, as there is little respite between major encounters. Talking to the Silph Co. employee in the room with the rival battle will net you a Lapras.

Continue to the top floor and defeat Team Rocket’s executives before facing Giovanni once again. Clearing Silph Co. ends Team Rocket’s occupation of the building and restores the company to its rightful owners, marking one of the major turning points in the story.

With Saffron City secure, visit the nearby Fighting Dojo. Defeating its master rewards you with a choice between Hitmonlee and Hitmonchan. The Pokémon you do not choose can later be found in the Safari Zone, so your decision is not permanent if you plan to complete the Pokédex.

Sabrina’s Gym specializes in Psychic-type Pokémon and remains one of the most challenging battles in Kanto. Bug- and Ghost-type attacks are the most reliable answers under Pokémon Scientist’s revised type chart, though careful team building is still essential due to her Pokémon’s expanded movepools. Defeating Sabrina earns the Marsh Badge and leaves only the final two Gym Leaders between you and the Indigo Plateau.

Chapter 10 — Cinnabar Island

Chapter 10 Spoilers

Pokémon Mansion is a sprawling dungeon filled with trainers, wild Pokémon, locked passages, and hidden items. Progress depends on activating a series of statues that open and close different doors throughout the building. Be sure to explore thoroughly, as the mansion contains several valuable items in addition to those required for the main story.

Your primary objective is to locate the Secret Key hidden deep within the mansion. This item unlocks the doors to Cinnabar Gym, allowing you to challenge Blaine. If you’re having trouble navigating the mansion’s layout, pay close attention to the effects of each statue switch, as revisiting earlier floors is often necessary.

With the Secret Key in hand, enter Cinnabar Gym and challenge Blaine for the Volcano Badge. His Gym continues to specialize in Fire-type Pokémon, though his team has been expanded and rebalanced for Pokémon Scientist. Water-type attacks remain effective choices, but don’t underestimate his improved coverage and stronger overall team.

Before leaving Cinnabar Island, take time to read the research journals scattered throughout Pokémon Mansion. Together, they reveal the origins of Mewtwo and document the events that led to the facility’s destruction. In Pokémon Scientist, these records tie directly into the game’s broader narrative and provide important context for the mysteries surrounding Team Rocket and Professor Oak’s research.

Chapter 11 — Viridian Gym

Chapter 11 Spoilers

With Blaine defeated and seven of eight Gym Leader badges acquired, enter Viridian Gym to confront Giovanni one last time. As the final Gym Leader, he fields a powerful and varied team that is considerably stronger than in the original games. In particular, Giovanni will use one-hit KO moves with abandon. Water-, Grass-, and Fighting-type Pokémon all have opportunities to excel, but his expanded movepools make careful switching and type matchups more important than ever. Defeating Giovanni also brings Team Rocket’s story to its conclusion.

Victory over Giovanni earns you the Earth Badge, completing your collection of all eight Gym Badges. Before heading to the Indigo Plateau, take time to make any final preparations. Stock up on healing items, finish any remaining side quests, evolve Pokémon that still need trade evolutions, and ensure your team is ready for the Elite Four. Once you pass through Victory Road, the toughest battles in Pokémon Scientist lie ahead.

Your rival awaits on Route 22 for the final battle before the Pokémon League. His team is the strongest it has been all game, featuring a well-rounded lineup with answers to many common strategies. Treat this battle as a final test of your party before entering the last Gym and make any necessary adjustments if you struggle.

Chapter 12 — Indigo Plateau

Chapter 12 Spoilers

Victory Road is the final dungeon before the Pokémon League and serves as one last opportunity to train your team. The cave is filled with powerful trainers, challenging wild Pokémon, and several valuable items. Although Moltres traditionally resides here, it will not appear until after you have become Champion, so you can focus entirely on reaching the Indigo Plateau during your first visit.

Heal your team and stock up on healing items before entering the Pokémon League, as you must defeat all four Elite Four members consecutively without returning to a Pokémon Center or accessing the Pokémon PC system. Each member has been significantly redesigned for Pokémon Scientist, with stronger teams, broader type coverage, and improved strategies. A balanced team with answers to a variety of threats is far more important than relying on a single powerful Pokémon.

After defeating the Elite Four, your rival challenges you for the title of Champion in the final battle of the game. This is the culmination of your journey and the toughest battle yet, featuring his fully developed team. Victory crowns you as the new Pokémon League Champion, unlocks the game’s postgame content, and causes several legendary Pokémon—including the legendary birds and Mewtwo—to become available for capture.

Postgame

Postgame Spoilers

With the main story complete, Gym Leaders across Kanto are ready for a rematch. Each leader fields a significantly stronger team than before, making these battles among the toughest in the game. You must defeat every Gym Leader at least once after becoming Champion before Professor Oak will propose a final challenge.

But before that, let’s have a little bit of fun. Travel to Vermilion Dock (did you notice how the S.S. Anne doesn’t leave after you get HM01?) and have a Pokémon surf across to the island on the right side. A mysterious truck is there; using Strength and then interacting with the truck will release a Level 70 Mew. It is prone to running immediately, but once it has been encountered, it becomes a roaming encounter. Mew will move to an adjacent route every 255 steps you take, and has a very low chance of appearing, but will retain the HP damage it took in any previous encounters. It also can’t run away if it is asleep or frozen.

Now that you are Champion, the three Legendary Birds become available. Articuno still resides within Seafoam Islands, Zapdos can be found in the Power Plant, and Moltres finally appears in Victory Road. All three have been strengthened considerably, so save your game before each encounter and prepare for long battles.

With the Hall of Fame recorded, Cerulean Cave opens for exploration. The dungeon contains some of the strongest wild Pokémon in the game and culminates in a battle against Mewtwo, now at Level 90. Bring plenty of healing items and your strongest team before attempting the capture.

Continue exploring Kanto to obtain every Pokémon. Between in-game trades, the Tradeback NPC, Safari Zone encounters, postgame legendaries, and the roaming Mew, every Pokémon can be obtained without trading to another game. Completing the Pokédex is required to fully complete Pokémon Scientist.

Once you have defeated every Gym Leader in their rematch and have obtained all 151 Pokémon, return to Professor Oak’s Laboratory. Satisfied that you’ve surpassed every challenge Kanto has to offer, Professor Oak finally agrees to battle you himself. His team represents the ultimate test in Pokémon Scientist, featuring powerful Level 100 Pokémon. Come prepared with your strongest possible team.

After completing the Pokédex and proving yourself against Professor Oak, return to the appropriate NPC to receive your Diploma, marking 100% completion of Pokémon Scientist. By this point, you will have conquered every major challenge the game has to offer and experienced all of its story, battles, and postgame content.