EDITED MARCH 14 2020: IT IS NOW THE COMPLETE "Glitch Quest" Guide for Time Anomaly's"
Brief Portal Locations:
snowtown
inside snowtown: snowtown bottom hill

swamp
inside swamp: swamp cave
^inside swamp cave maze

under ctf
^inside this portal in fox tunnels (air asia access)

delta island

deadwood

on the way to snowtown from onnet (through cave by school)
^inside this portal but in the witch forest

bridge before york
york near pyrats

castle

FINAL PORTAL: the center of graal city near the entrance

Deadwood Time Anomaly
Begin by going to deadwood portal and find the bank. You need to rat morph to get into the safe and grab a rusty key. Then go into swamp portal and head far right to find the miners. Enter the cave until you find another portal within it. From there you need to find a cave part that needs a rat morph to enter this cave maze. From there you need to find another portal that will take you to a doorway where you will have to complete a stealth mission to destroy bush town from being formed. You have to avoid being seen and destroy these huge bushes with your sword (they are like a tower flag). You can hit some bush people npc and they will get stunned. Not all 3 of the huge bushes have to be destroyed at once, so you can take it slow when doing this. When you destroy all 3 bushes to complete the mission you have to push a box in the top left corner to release some prisoners. When you complete this, head back to present time deadwood and the hourglass will be there.

Onnet Witch Time Anomaly
Begin by heading into the portal that is between onnet town and snow town path near sardons tower. Head up to where the witch is originally in the trees and get past the tree maze to find the portal to her. Speak with her and then head exit and head to the swamp portal. From here talk to the witch in this past time line and she will give you a recipe in which you have to find and ingredient for. You will need 3 ingredients, which are a lifebug, honey bee, and a green butterfly. I think they spawn in a random in these 3 locations: 1 in delta portal, 1 in portal under ctf, and 1 in air Asia (use the air balloon in graal city from located in the fox tunnels in ctf portal). After you bring here these ingredients for her 3 recipes, bring the potion back to the witch in onnet tree maze. You will get a rat morph. When you complete this, head back to present time onnet tree maze and the hourglass will be there.

Nexus Time Anomaly
Begin by heading into the portal that is between onnet town and snow town path near sardons tower. Head down to around where the fun cave is and where the path to sardons tower begins and you should notice that an npc is throwing red bombs. You need to grab one of them and bring it to a broken pillar that is in the caves above mod town with out dropping it. Proceed to grab the bomb and make your way out of the portal back to present time and head towards the portal under ctf. When you get here, head north into the caves and continue north following the railway tracks. You can walk along the track even though it may seem there is a hole in the ground just don’t drop the bomb. Follow it until you reach a broken looking pillar on the right side where an npc should be standing. Throw the bomb on that pillar and it will explode. Congratulations you have destroyed a cult looking to find some relic and saved nexus! After you complete this you will be teleported out. From here head towards York and there will be a portal right before York bridge near the grotto. When you enter this, the cult will be gone, and nexus will be there. Inside nexus is Japanese theme. When you complete this, head back to present time nexus and the hourglass will be there.

Castle Time Anomaly
Head to the castle and the portal should be to the right near the front gate near stables. Head in and find the flag room. Find the broken flag in there. Head to delta portal and head towards the castle. Show the chad guy the flag and he will let you in. From here you must slowly make your way to the flag room and reclaim the castle. You cannot proceed to the next room because dead guards will block the door until you kill all the invaders (if you turn nicknames off you can tell who the baddies are). I recommend eating food in between here since if you die you must start at the beginning of the castle again. When you get to the throne room, eliminate all targets then hit the flag until 0. When you complete this, head back to present time castle and the hourglass will be there.

York Time Anomaly
Start at snow town portal. Make your way down the map to this snow hill. Stay on the left side and you will slide into the next time portal. When on the cliff side, make your way down the cliff and as far right as possible then head north to find a tombstone. Push it up and stairs will appear. Follow this path until you reach the summer house. Go inside and go to the left room and talk to the npc. He will give you a chest in which you need to hide. You need to dig a hole and equip the chest to put into the hole. You have to try different spots underneath the summer house, but not past the fences until you bury the chest. Head back to that npc and he will give you a flyer. Take this flyer and head right through the water until you find a pyrat. Hand the flyer to him and then go back and talk to the npc. Now make your way to the York portal that is near pyrat bay in present time. Head in and go back to the summer house. The npc should give you a gold gralat and explains that this treasure hunt idea caused the pyrats to invade York. When you complete this, head back to present time York bridge and the hourglass will be there.

FINAL PORTAL: Center of Graal City
ITS FINALLY HERE AHAHAHAAHAH THE FINAL PIECE OF THE PUZZLES!!!! -MARCH 14 2020

There's also hats they added in old school revolution here but explore and go find it yourself!!!

Use all 5 of your hourglasses from the quest folder near the portal in the center of Graal city. go into the portal and make your way to Sardons tower. Head to the top like where flag room is.
PRO TIP:
IF YOU SEE POTS GRAB THEM BECAUSE YOU GONNA NEED AS MUCH HEALTH AS YOU CAN SO THROUGH THIS WHOLE PART SO YOU DON'T GET SENT BACK TO THE BEGINNING (ALSO WILL HELP TO NOT HAVE LOW AP CUZ IDK IF YOU WILL HEAL IN HERE WITH LOW AP). FOOD ITEMS AND MEDITATE WONT WORK IN HERE.

You now have to do this obstacle course thing. For the first part you can either dodge all the rocks shooting yourself or pull and pull the statue and use it as a shield. Statue pulling/pushing will be a recurring theme while you spend your time in here. Next is the spike rocks that move towards you when you are in their vision. Just bait them out by making them move towards you then move away. Walk behind them to progress through this part since they don't move as fast when they are coming back (just like regular Sardon/Destiny tower ones). Now there's a small boss fight. Just run circles around the boss and hit him. The portal in the middle will try and suck you in during the whole fight. After you kill the red baddie, let his body get sucked into the portal and both doors will open.

YOU CAN EITHER GO LEFT OR DOWN HERE. I RECOMMEND GOING DOWN FIRST BECAUSE YOU WILL HAVE TO COME BACK TO GO LEFT LATER
The left door takes you to a side room where you have to find the correct statue to pull. If you go to the wrong statue it becomes a time bomb that follows you so run away. The correct statue is holding a shield. pull it to the middle button then the door on the left opens. Now in this next room there's a top door that you need a key you will get later on to open it, and a bottom room. The bottom room literally just contains chests with some red gralats and bombs and arrows. Basically just run in between the spaces of the fire moving around to get to them, then do the same thing again to get out.

The bottom door takes you too a room with arrows shooting on the walls and baddie that shoots arrows and imitates your movements
HEAL UP and make your way through the room. you can hit the baddie then just run through him and then heal up at the end again. This next part takes a lot of timing and patience. You have to move a statue from the top right of the room to the bottom left button, all while not being killed by turrets shooting rocks at you. I recommend moving the statue little by little to get to the button, and I don't think the statue can go on the glitched ground so you basically have to go left, then down. If you health is getting too low just go back up to the room above to get health, but you will have to restart the whole process of moving the statue again.

When you get the door open, you will end up in a room with only the top door open and fallen rocks blocking the bottom door. We will be opening up the bottom part with rocks. Go into this door. You will notice there's 2 portals and some chests at the top. Grab the chests and then go into the left portal. It will be a dim lit room and the statue you need will be at the top right corner. Move the statue to get it into the portal. Now go into the portal and move the statue into the right portal. Notice where the button is while inside this portal and move the statue to that button to open up the door on the bottom. Go into that door. You should now be in a small room where you just need to push a statue down. Move the statue to that button, and notice the rocks on that bottom door move a bit. Now leave and go back to the room I mentioned earlier that was before the room with 2 portals in it. The door on the bottom that was covered by rocks is now open. Go in.

This part is very important, as you will notice there is a key you will want to grab out of this obstacle course. Heal up and make your way through the course. If you happen to take a lot of damage early I recommend trying to get back to the health pots again. Dying here sucks because you restart everything........ Well once you get the key and the optional chests, you can either walk back or kill yourself to get back to the front, but it doesn't matter. You just have to get back to the room where you kill the red baddie.

Once back at the room where you kill the red baddie, head into the left room. If you didn't go in here earlier refer to my instructions above. Open the door that requires a key now. (AT THIS POINT YOU HAVE A CHECK POINT SINCE YOU HAVE OPENED THE DOOR AND YOU DON'T HAVE TO GET THE KEY AGAIN)

This room looks deadly with the turrets and the golden baddie. I recommend getting the baddies aggro, and getting him come to that right wall near the pots. You can hit him here if he is touching the wall and he will not be able to hit you, and you will be able to heal a lot. Once you kill the baddie just run through all the doors until you get to a part where you have to jump down this ledge. This is now the checkpoint for if you die while fighting the boss, which I will explain below.

GLITCH WORM BOSS FIGHT
Jump down the ledge and enter the portal. You will now be at the boss fight arena. This is finally the climatic fight between Graalian and the "bug" responsible of all the glitching that is happening through out Graal. Wait a little bit and the boss will show up. His pattern is he will come out of a portal and that portal will shoot various objects out at you. Don't get hit by any of them. You also can not touch any object on the ground except for the pot, sign, and bush. You must pick one of these up and throw them into the portal to close the portal and prevent the boss from entering it. The pot is recommend because when you pick them up, they drop you health still. Once you close the portal and the worm can't enter, it will start moving around on the ground. Hit the tail as many times as you can before it enters another portal. The goal is to get rid of all the sections on it's body, via hitting the tail. Rinse and repeat the method. When you beat it, a green chest will appear. Collect the chest and you will get the "Corrupted Screen" effect!

Thanks to Mercy (Re) for the help on the boss fight!


Extra (Free Items)

Guaranteed Glitch Keys
There are glitch chests that are hidden in each portal that require a glitch key to open.
In addition to these, you can also get guaranteed key from moving these boxes left of where you come out of the portal between onnet and snowtown. Iv been told it is easier to do on pc than on mobile.
It also appears you can get a key from killing those purple glitch worms, but I have yet to obtain one.

Thanks to Yami for this fantastic list he created for the guaranteed key drops and Numbrero for finding the 10th key!

Glitched Chest Locations and Items
YOU NEED GLITCH KEYS FOR THESE. THESE ARE GLITCHED CHESTS. Seems like the chests are the same for everyone. Appears to be total of 10 chests and 10 keys from what I have gathered?

Glitched Mount
Go into the ctf portal, then go into the fox tunnels all the way out till you see the air balloon to air asia. You need to enter the building before the air balloon then head left until you reach this little grassy area with a rock border. In the top right corner there is a rock you can bomb (has a brown dirt patch under that not grass.) Bomb this rock and head inside, and that chest contain the glitch mount.

Glitched Bow
Go to snow town portal and head up past the getaway resort. There should be 2 trees with a door between them. This is the snow town pk zone, and inside you will take a teleportation spot to the location of this chest.

Glitched Bomb
Go to swamp portal. Make your way towards the miners but don't head into the cave. Stop around the slope near the waterfall. This one is sort of difficult to explain, but you have to go down and find this little brown patch right against the cliff edge, south east of the small waterfall that is there. In this specific spot you can jump on to the cliff, then head left and the chest will be there.

Glitched Burgers (5 of them per chest)
Navigate the swamp maze cave. You will eventually find the chest in there.

Get to air asia via the ctf portal and fox tunnel portal. When in air asia go far right to around the bottom right corner where there is a lot of bushes. Make your way through and the chest is there.

Glitched Egg Hat
Go into the portal that is between onnet and snow town. Go to the school and get to the roof. You will see the chest from the outside.

Glitched Santa Hat
Go into the Delta railroad (you need a train to get to this one). Use your train to go to the right until you see a chest.

Glitched Cowboy Hat
take ctf portal. Go up to the rail roads again and follow them to the left until you see a chest.

Glitched Straw Hat
Take the delta island portal and go to the castle. When inside take the right stair case to the basement around where the hat shop is. Instead of going to the hat shop, head straight down to this storage room and the chest is there.

Glitched Pluffy Hat
Once you finish the york time line, go into the portal that is at york near the pyrats. Head far right in the water until you see a pirate ship. The chest is on this ship.

Glitched Screen Effect
Beat the "bug" Worm boss in sardon's tower 2009 via Center Graal City portal.

Treasure Hunt Trophy
Apparently if you go into the york portal near pyrats, you can dig up the treasure you buried in the past and you will get a trophy furniture. Thanks to Reggie* for the information.

There are also npc's that will ask you to help them. If you do answer their questions successfully you will get an honor point like the old days. If you fail they will disappear. Honor points can be used in the honor point shop which is located inside the delta portal. Seems like if you fail they come back though somewhere else? Not too sure though.

Hopefully this helps you complete the entire quest line up to this current date. Sorry if i missed anything but I'll add things as I find out more!