There are a total of sixty-two "substories" in Yakuza 4, with a sixty-third available once the others have all been cleared. These appear in your status screen under the menu of the same name, and are essentially side quests. You can ignore substories entirely if you so choose and still complete the main game, but completion of various substories unlocks minigames, provides bonus gear and experience, and provides hours of additional gameplay.
A couple of side missions kind of look like substories—particularly Kiryu and Tanimura's dealings with Akaishi and the Kamurocho volunteer squad—but don't actually count towards that total.
LAYOFF ALREADY Edit
You receive the call for this substory while you're on your way to meet Kido in 1-2. Return to Sky Finance at any point thereafter to meet Shiohara, a prospective customer. Give him all three of Akiyama's tests, one after another, until you get the option a fourth.
Afterward, go find Paradise Advertising on Shichifuku Street West. Its president is standing by the side of the street with a green arrow over his head. Speak with him, then go find Shiohara in Children's Park and defeat the Angry Ex-Employee.
As a reward, you'll receive 5,000 XP and the Memoirs of an Action Star, an item that shows up in the Valuables tab of your inventory. It provides three weapon designs.
HOW TO SPEND MONEY Edit
You'll probably run into this substory in 1-2, while you're heading to meet Kido. Shoko Muto is in an argument on Taihei Blvd West, north of Sky Finance, and needs somebody to lend her money. Talk to her after her argument concludes, and she'll meet you back at the office.
After you speak with Shoko, go to Adam, a host club in the hotel district, and Le Marche and Sushi Gin on Showa Street. You'll need to beat up a few loan sharks while you're at Adam, two of which are armed. Once you've seen Shoko at all three locations, meet her back at Sky Finance. You'll receive a Protective Amulet and 3,000 XP.
ART OF SCOUTING Edit
During the day, look for the Lame Scout outside the Club Elise on Taihei Blvd. You now have five minutes to get three girls' phone numbers, so speak to as many of them as possible. The timer is still running while dialogue boxes are open, so try not to talk to anyone else; it wastes time.
You'll probably have to beat up a couple of jealous boyfriends, but the key to finishing this in time is mostly just being thorough. Look for women with green arrows above their heads, and be flattering; compliment them on being attractive if the choice comes up. Complete the challenge in time to earn 5,000 XP.
PIMP MY OTAKU Edit
Starting in 1-3, there's a guy named Taniguchi outside the Elise on Taihei Blvd. Talk to him, then go meet him later on south of the Millennium Tower. He's... not doing well.
Pick whatever option you prefer to dress him up differently, and advise him to listen to what the hostesses are saying. Taniguchi will reward you for your tutelage with Shiny Shine! Love Shine!, a magazine that provides you with two different designs for kali sticks.
MAKE IT BIG WITH FX Edit
At the start of 1-4, you get an email on Akiyama's phone discussing a suspicious opportunity to invest in foreign currencies. The people hawking the scam are on Senryo Avenue, on the southwest edge of town. Tell the guy on the street you came by to hear the talk.
If you opt to sign the contract, you receive 2,000 XP. If you don't, you have to defeat Sagi, the company's president, and his band of thugs. This gives you a great opportunity to beat up a lot of people with very fragile office furniture, in addition to 2,000 XP and a 40,000 yen bribe to stay quiet.
GOURMET REPORTER Edit
At the intersection of Taihei Blvd. East and Pink St. near Elise, there's a guy with a stomachache lying in the middle of the street. Talk to him to help him out.
This is Ajikawa the food reporter, and he asks you to bring him information on the tastiest dishes in Kamurocho. Until then, he's warming a barstool at the Earth Angel in the Champion District, which may tell you something about him.
What this boils down to is a memory test on various dishes at Kanrai and Kyushu. At Kanrai, recommend the Grade A Sirloin and the Grade A Harami.
The next time you visit the bar, Ajikawa gives you 50,000 yen, and now wants information about Kyushu. They use tonkatsu stock and top their ramen with spicy roe; tell him as much. When you come back to the bar, he gives you 50,000 yen and a Diamond, and you receive 5,000 XP for completing the substory.
THE FATE OF THE 30 MILLION YEN Edit
After you've helped Shoko in "How to Spend Money," the Desperate Man appears in the New Serena Backlot. Approach him to begin the substory. After you agree to help him, go wander around the city for a couple of minutes until you receive his call. Return to Sky Finance to get a briefcase containing 30 million yen.
Go meet Nishihama at the lockers on Taihei Boulevard. Opt to follow him to West Park, then go talk to Miki's Friend at Children's Park north of Theater Square. From there, go to Le Marche on the south side of town. You'll see Miki, who runs off.
If you ask some of the passersby, you'll find out Miki went to Theater Square. Talk to the Angry Student in Theater Square to find out Miki went north. Speak to the taxi driver near the M Store, then head a bit further north to automatically enter the Red Brick Hotel. Beat the pudding out of Nishihama to receive a Gold Plate and 5,000 XP.
THE APPRENTICE Edit
After you clear "Layoff Already," return to the street outside Sky Finance to find Shiobara. He wants to be Akiyama's "apprentice." Beat the snot out of the drunken guy who comes in shortly thereafter. You'll receive 5,000 XP.
LONELY HANA Edit
Once you've completed "The Fate of the 30 Million Yen," go by Kanrai. Akiyama will buy Hana lunch. Bring it to her at Sky Finance for a cutscene.
Now you have to track down somebody who's into "rounder" women. Check all four of the options Akiyama comes up with—MEB, Theater Square, Elise, and the Club SEGA on Nakamichi Street—and speak to people in each location.
At the last place you look, you'll hear about a hostess scout who's looking for chubby girls from a Grumpy Owner. Go find him and bring him back to Hana for 5,000 XP.
THE APPRENTICE: PART 2 Edit
Visit Theater Square after you complete "The Apprentice," and you'll meet Arima, one of Akiyama's competitors. After your meeting with him, return to Sky Finance for a scene with Shiobara.
Head to his office, which is across the street from the M Store, and kick Shiobara's teeth in.
AKIYAMA VS. HOSTESS CLUBS Edit
Minamizawa the comedian and his long-suffering producer are in MEB on Shichifuku Street, and need somebody to help them explore the hostess scene in Kamurocho. That's apparently where you come in.
In order to be able to provide information to Minamizawa at all, you must visit each club at least twice; once to get a girl's card, and once to request that girl specifically. Some of the answers he wants only seem to pop up when somebody else is visiting the same club, so you may want to try visiting as another character. Minamizawa gives you 10,000 yen for every right answer you feed him, and 5,000 XP when you've given him all the information you can.
Visit the clubs Jewel and Shine a few times and get to know a few of the girls there. Noa likes ballet, chicken, and good drivers; Erena is from Kyoto, drinks Yamazaki 12-year-old whiskey, and is into manly rich guys; and Rio likes rose champagne, has a dog, and wants to be a pin-up model.
A WIFE'S CONCERN Edit
After you've dealt with Shiobata during "The Apprentice: Part 2," Setsuko Arima shows up at Sky Finance the next time you stop by. When she leaves, run over to Elise, just in time to cave Arima's face in. Once you drop him, this substory's done, and you earn 5,000 XP with relative ease.
COUNTERFEIT BILLS Edit
You must complete "Lonely Hana" for this substory to begin. Return to Sky Finance to hear news of counterfeit money making the rounds, and to meet Hayashida.
Take the copies of Hana's sketch around to Sushi Gin, Poppo Nakamichi Street, Volcano, and the homeless "village" near West Park. Once you've visited all four locations, your homeless buddy will call you to alert you to the counterfeiter running around Pink Street. Go chase him down.
Rest until nightfall at New Serena, then take a taxi to the docks. Take out the group of yakuza there to do your civic duty and earn 5,000 XP.
TRICKS OF THE TRADE Edit
After you deal with Shiobara's issues in "A Wife's Concern," you'll run into him at the south end of Tenkaichi Street, and Akiyama challenges him to a game.
For your end of it, trade the Cigarette to the Nicotine Yakuza across the street for Stomach Medicine. Give that to the Nervous Man near Smile Burger on Nakamichi Street for Concert Tickets, and give those to the Celeb Guy on southern Tenkaichi Street by the taxi stand in exchange for a Business Card. Swap the card to the Regretful Man in Theater Square for an Expensive-Looking Watch. You'll receive 10,000 XP... but unfortunately, you don't get to keep the watch.
BEWARE OF IMPOSTORS Edit
After you clear "Counterfeit Bills," go to southern Theater Avenue and look for a sharp-dressed, angry man. Speak with him, then go north to find another dissatisfied customer.
The fake Sky Finance office is in Park Alley near Kamiyama's weapons shop. Go on inside, and when the time comes, pummel the Masked Men. The rest is just a series of dialogue scenes, ending in your receiving a Super High-Voltage Battery and 5,000 XP.
HOSTESS TRAINING Edit
After you've successfully pimped your otaku, return to Elise. Miki's got problems, and you need to fix them. Talk to the employee outside to meet her in the back room.
Advise her to be more open on dates, and ask for her date's favorite dish. Further, create an at-home atmosphere, then take out your wallet like you're going to pay. You'll receive 5,000 XP.