https://i.imgur.com/JNChd.pngThe side deck is so that you can stop top tier and meta in matches. The side deck can easily get rid of Dark World, and it can stop Wind-Ups. Being able to stop the two main archetypes to side deck, it can stop all the other little problems too and control the field.
The extra deck is to easily gain power in the field. It is also so that you do not have only one option, no matter what your hand.
Side Deck:Two Gemini Imps - This is so that if you are dueling Dark Worlds, your opponent does not get a draw, but you do. It also stops them from going for Grapha. This also helps hand destruction decks.
Two Maxx "C" - The basic card in a deck. It is to get a good hand from swarm decks. Also, if you use it at the right time, your opponent will limit how much they special summon, compared to if you did not have Maxx "C".
One Mystical Space Typhoon - Just in case I duel a Hero deck (Since they use a lot of traps). It also helps against decks that focuses on removing from play your monsters. Also, three MST is good in a deck, but to provide space in the main deck, I decided to put an MST in the side deck.
Two Dust Tormado - Basically the same idea as MST. If you have a trap in your hand that you feel can help adjust the duel, then you can play Dust Tornado to use its affect to set a card. Dust Tornado also can be used as a well played bluff if you use it at the right moment.
Two Gozen Match - This is to control the field, and limit what your opponent can do. This restricts them from playing other monsters with a different attribute, limiting the monsters they can have on the field.
Two Needle Ceiling - This is so that if you are dueling a swarm deck, you can easily get rid of the cards your opponent summons. It also helps if you are about to get OTK'd or if you are about to lose a duel due to the fact that your opponent has 4+ high attack monsters.
Two Royal Decree - This is to negate your opponents traps that would ruin your hand, field, or your plays. This also helps against cards that mess up your summoning, like Bottomless Trap Hole, Torrential Tribute, and Compulsory Evacuation Device.
Two Shadow Imprisoned Mirror - This is to side against Dark World, and anyother dark archetypes that have effects in the Graveyard.
Extra Deck:Two Gem-Knight Citrine - This is to finish off your opponent without having to worry about their traps. It is also Level 7, so you can use it for XYZ summoning. It also helps to get some damage into your opponent.
Two Gem-Knight Prismaura - This card is to control your opponents field, and to control your own field and graveyard. This is a better version of Scrap Dragon. It can use its effect more than once per turn, and it helps to get some Gem-Knight cards in your Graveyard to active some effects of the Gem-Knights. It also helps with the Lightsworns in the deck because of Lumina. It is also level 7, so it is good for XYZ. Also with the right combo, (having a lot of monsters in your grave and Gem-Knight Fusion in your hand) you can destroy your opponents whole field so long as it is face-up.
One Gem-Knight Seraphi - This card helps to get out other monsters on the field to start an OTK.
Gem-Knight Zirconia - This is a high attack fusion monster that is easy to get out. It is good to get rid of most of your opponents monsters, and it helps get some damage in.
One Leviar the Sea Dragon - This is to recycle the monsters lost in the removed from play zone. This helps get back monsters lost from Gem-Knight Fusion and it can get back monsters lost from decks that focuses on removing from play your cards.
One Daigusto Emeral - This recycle monsters in your graveyard lost from Gem-Knight Fusion, Lightsworn, and battle. It also helps you draw if you are in a tight situation. If you have a normal monster in your Graveyard, then you can use this effect to get it on the field.
One Maestroke the Symphony Djinn - This is like a Zenmaines, but works against Stardust. If you're opponent has a high attack monster on their field, or has a lethal effect, then you use Maestroke to get rid of it.
One Number 11: Big Eye - This is to take control of your opponents monsters, and control their field. This helps if your opponent has Black Luster Soldier on their field, or Blue-Eyes Ultimate Dragon. It also helps get rid of any other high attack monsters. You can also use it to take control lethal effects, and get it also helps you get an XYZ or synchro out with your opponents monster. It also helps you get out the Gem-Knight fusion monsters.
One Lavalval Chain - This is to get some monsters from your deck to your Graveyard, and a monster from your deck that you want to draw. Also, with the right effects and combos, you can use its effect to swarm your field with monsters.
One Catastor - This card is to shaken your opponent during the duel. It can limit what your opponent summons, waste their cards, and it can get rid of monsters like Black Luster Soldier.
One Iron Chain Dragon - This card is good to waste your opponents deck, and has good ATK so it can get through most of your opponents monsters.
One Black Rose Dragon - This is to nuke your opponents field and get rid of cards that are hard to get rid of with a normal hand. It also has good ATK and is level 7, so it can be use for Number 11: Big Eye. It can also be used to bring out Gem-Knight Cetrine.
One Scrap Archefiend - It is a level 7 monster that is easy to get out with high ATK. This can start an OTK and get some damage done to your opponent. Also, it can get rid of most of your opponents monsters like Stardust Dragon. It too is level 7, so it can be used for the XYZ.
Subject: Obelisk blue lesson 3: side and extra deck! 
