Once Skarmory is defeated, Diglett is safe and you are free to head back. Magnemite wants to join your team, but there isn't a place where it could live. After you are back in Pokémon Square, Friend Areas will be unlocked after a short talk with Magnemite and Wigglytuff. Now you can buy Friend Areas at the Wigglytuff Club and pickup new recruits. Magnemite joins your team after Wigglytuff gives you the Friend Areas Mist-Rise Forest and Power Plant for free. Magnemite goes to live in Power Plant.
The Friend Areas for you and your partner will automatically be unlocked.
Complete at least three rescue jobs to encounter an event with Team Meanies. They will "steal" all of the rescue jobs in your mailbox (they will still be there anyway). Pelipper will bring another job to your mailbox immediately after. Complete two more rescue jobs to bring Caterpie to your base. He will explain that his friend Metapod is trapped in Sinister Woods, and how he wants you to rescue him. Team Meanies will come up behind you, and say they will do the mission instead. Take some time to train your team. If you want, take a new recruit to Sinister Woods. It will help on the boss fight.
Sinister Woods Pokémon
This dungeon is a little harder. Remember to bring several food items like Apples and few Max Elixirs to restore PP. Having a third team member makes clearing the dungeon easier.
Once you reach floor 13, you will have to defeat Team Meanies. If you are having trouble with this battle then you may need to level up more or bring more items.
You might need to use some tactics to defeat your second boss. If you have Magnemite that joined your team, it will be easier as Magnemite resists all attacks that Team Meanies have. Gengar is dangerous because of its Curse and Hypnosis. Medicham has ThunderPunch, but they won't be dangerous because Medicham is Team Meanies' lowest leveled member. Ekans can be annoying, but it shouldn't cause any problems for high-leveled teams.
After defeating Team Meanies, Metapod appears and is rescued.
When you wake up, head to Pokémon Square and watch Jumpluff beg Shiftry to create wind so another Jumpluff can escape from Silent Chasm. Team A.C.T. will then come and make Shiftry go.
Complete Rescue Missions, train your team or recruit new team members until Jumpluff will come to your team base and say that Shiftry never came back. Jumpluff will take you to the entrance of Silent Chasm. At the entrance, you will be asked a number of questions, and no matter what you answer, it will lead to your rescue team going into Silent Chasm to rescue Shiftry.
This dungeon is quite hard if you aren't prepared. Most of Pokémon in Silent Chasm hit hard and may cause some problems to inexperienced players. If you want to play safe, train your team more before going to Silent Chasm. You should watch out for Beedrill, Dustox, Yanma, and Farfetch'd.
At the end of Silent Chasm you will meet Zapdos. You will be able to save Jumpluff without a fight, but Zapdos flies off to Mt. Thunder with Shiftry.
After rescuing Jumpluff, head to Pokémon Square. Everyone is worrying about Shiftry. Your team and Team A.C.T. decide to scale Mt. Thunder and take Shiftry back. When you arrive at Mt. Thunder, your partner will be wondering where Alakazam's team went. Your partner will then speak of how tough fighting Zapdos sounds. No matter how scared your partner is they'll get over it and the two of you will be ready for quite a battle.
If you are prepared, this part of Mt. Thunder won't be difficult. There are some dangerous Pokémon like Electabuzz, but you shouldn't have many close calls.
Mt. Thunder Peak
When you get to the 11th floor there will be a save point where your belly and your HP goes up to full.
Mt. Thunder Peak has some dangerous Pokémon, but it's fairly short with 2 floors plus Zapdos's area.
Before you can rescue Shiftry, Zapdos must be defeated.
This will be a hard fight. Agility boosts Zapdos's Movement Speed, allowing it to effectively move and attack in the same turn, making tactical retreat to heal useless. Thunder Wave can be annoying, so Cheri Berries will be useful. Peck and ThunderShock hit hard, but if you're lucky, Zapdos won't use them at all. Wonder Orbs can't be used in boss rooms, but Gravelerocks and other useful items can be.
After Zapdos is defeated, you will be able to rescue Shiftry. Team A.C.T. will then show up, and Alakazam will reveal that he can tell you're a human, and suggests you to go to the top of Great Canyon and meet Xatu.