In Saints Row: The Third, you will have to make important decisions that will affect what reward you will get for certain missions. In this guide, I will explain the outcome of all of these choices, as well as explain which choices I personally recommend.

Keep in mind that I prioritize the actual rewards over the story elements affected by the choices.

At the end of the mission, you'll have to decide whether you want to destroy the Morningstar building, or keep it for the Saints.

DESTROY the Building

• 10% permanent respect bonus whenever you earn respect.
  
• You'll earn the "Kuh, Boom" achievement.
  
• Altered ending cutscene where you drive to Gat's funeral.
  
• The tower will be destroyed for the rest of the game.

KEEP the Building

• 10% permanent cash bonus whenever you earn cash.
  
• You'll earn the "Tower Defense" achievement.
  
• Altered ending cutscene where you settle in your new tower.
  
• The tower will be there for the rest of the game, and will glow purple at night.

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IMPORTANT: If you want both of the achievements, create another save before starting the mission so you can redo the level and get the other achievement.

I personally recommend keeping the tower for the extra money bonus. Money is much more important than respect, since you will eventually reach max respect by the time you finish the game (and you can even purchase a bit of respect with cash). There are many ways to spend your money (weapons, vehicles, upgrades) which is why it's always good to have a lot on you.

Near the end of the mission, you'll get a call from Matt asking for the hos back. You can either bring them to Matt, or keep the hos for yourself.

GIVE the hos to Matt

• $25,000 will be given to you immediately.

KEEP the hos for the Saints

• $1,000 will be earned every hour for the entire game.

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Keeping the hos for yourself is better in the long run. It will take a while, but eventually you will make more than $25,000 by keeping them, as opposed to just receiving $25,000 on the spot.

After you beat Matt in the simulation, you'll have the option to go through one of two doors. One will give you a permanent discount on vehicle upgrades, while the other will give you a permanent discount on weapon upgrades.

VEHICLE door

• 50% discount on all vehicle customization.

WEAPONS door

• 25% discount on all weapon upgrades.

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Going through the weapons door is the better choice in my opinion. Weapon upgrades already cost a ton of money so it's good to get a discount on them. Only go through the vehicle door if you purchased every weapon upgrade, or if you customize vehicles on a regular basis and have no interest in weapons.

While protecting Josh from STAG, Cyrus will come up to you and give you the option of handing over Josh to STAG. Despite Shaundi's objections, you can give Josh to her for the Saints.

GIVE Josh to Stag [Cyrus]

• STAG territory assistance: have STAG take over a single district for the Saints
  (no need to do the random activities in the area).

KEEP Josh for the Saints [Shaundi]

• You'll unlock both Josh Birk AND Nyte Blayde as Homies.

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Giving Josh to Shaundi is the much better choice. You can gain all territory by doing fairly easy activities, so the STAG takeover is a bit useless. You can only get Josh and Nyte Blayde by keeping him in this mission which is why it's better to do so. Keep in mind that you can have both Josh and Nyte Blade fight with you at the same time (even though they're the exact same person).

While disguised as Cyrus, you'll be shown three different STAG products that you can have: you'll only be able to choose two of them.

Satchels

• Throwable explosives that can be detonated at any time.
  
• Can NOT be obtained by using cheats.

Specter

• A STAG hoverbike for you to fly around in.
  
• Can be obtained by using cheats.

S.T.A.G. V.2

• An improved STAG tank that has 50% more firepower and a slightly different paint job, but is still just as slow as any other tank.
  
• Can NOT be obtained by cheats, though regular versions of the tank can be obtained regularly.

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Always choose the satchels, since they are an amazing and hilarious weapon to use, and because they can only be obtained through this choice. The other choice is up to you, but unless you want to use cheats, I would choose the specter since it is much more useful and fun to use. The only thing that makes the tank different is it's color and slightly stronger firepower; aside from that, it's just like any other slow tank that you can find regularly, which is why I don't recommend choosing it.

Once you have the truck with the zombie virus, you are given the choice to either destroy it for Burt Reynolds, or keep the virus for the Saints.

DESTROY the virus

• Both Burt Reynolds and S.W.A.T. officers can now be used as homies.

KEEP the virus

• You now have zombie homies to use.

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Destroying the virus is better since you unlock two homies: S.W.A.T. officers which are useful, and Burt Reynolds (why would you not want him on your team?). Zombies are ok, but you'll unlock Zombie Gat when you beat the game so choosing them is kind of pointless.

It's now time to take down everyone's favorite green luchador, Killbane. What better way to do so than by humiliating him on live TV? The real question however is, will you do so?

UNMASK Killbane

• You now have Killbane's mask to wear, taunting while wearing it will cause people around you to burst into flames. Can't be obtained with cheats, though you can upload and download a custom character wearing it.
  
• Ending cutscene is different, as Killbane is unmasked and runs out of the ring covering his face.
  
• Killbane will no longer wear the mask for the rest of the game (obviously)*.

*Even if unmasked, Killbane will always be wearing the mask when running to his jet during the last level since that scene is pre-rendered.

SPARE Killbane

• You now have the Apoca-Fists as an equippable melee weapon, makes people explode upon punching them. Can be obtained by cheats.
  
• Ending cutscene is different, as Killbane taps out and leaves the ring.
  
• Killbane will continue to wear his mask for the rest of the game.

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This one is hard to choose. If you are deciding just for the items at hand (and assuming you don't like to use cheats), sparing Killbane is probably the better choice. I personally prefer the Apoca-Fists over the mask since they are much more amusing and more useful in combat. Though as stated before they can still be obtained with cheats. The mask is also nice to have, and unmasking Killbane definitely suits the story more, though in the end the Apoca-Fists are more fun to have.

Now for the final decision. While fighting off the many enemies, you'll be given a choice: save one of your best friends, or defeat Killbane once and for all.

ONCE YOU COMPLETE THE GAME WITH ONE OF THE CHOICES, YOU WILL BE ABLE TO SELECT THE OTHER CHOICE FROM YOUR PHONE AND RECEIVE THE BENEFITS FROM THAT CHOICE AS WELL. IN OTHER WORDS, DON'T WORRY ABOUT THIS DECISION AT ALL!

Save Shaundi

To save Shaundi, you'll have to climb to the top of the statue and use a throwable item such as fart in a jar to free her and defeat Kia. Upon completion of this mission, you'll automatically start the mission Gangstas in Space.

The following rewards are earned for completing Gangstas in Space:

• The "Gangstas... In Space!" achievement will be unlocked.
  
• You'll get $100,000.
  
• Your gang can be customized to have space Saints.
  
• Space suit costume can now be used.
  
• The Saints Raider vehicle can now be used.

Kill Killbane

If you want to kill Killbane, you'll have to ride with Angel and shoot down Killbane's plane. Once you do you'll have to do a small QTE and watch as your friends get blown up. You'll then unlock the mission STAG Film.

The following rewards are earned for completing STAG Film:

• The "Too Close to the Son" achievement will be unlocked.
  
• You'll get 100,000 respect.
  
• STAG armor costume can now be used.
  
• Cyrus' VTOL (jet) can now be used.

I hope this guide served a purpose. I'd like to thank Saints Row Wiki[saintsrow.wikia.com] for providing most of the pictures in this guide, as well as providing a few of the completion rewards. If you feel that there is room for improvement in this guide, please say so in the comments.