Pokemon Glazed (Side Quest and Legendaries)

Lance- (After Johto League) Head to the peak of Victory Road and speak to Lance. He will ask you to meet him at the train station in Goldenrod city. Head to the train station and talk to Lance. A mine cart will come rolling along and you get to ride it. Head north into Mt. Silver. Use rock climb to go up then go east and go down. Head west on the tracks into the next area and pick up the magnet. Head back and go south then east and use rock climb. Follow that path and you will climb down twice then head into the next area where you will climb up once more. Follow the path into the next place and go all the way north where you get to capture Heatran. You now have one of the prerequisites to catching Groudon!

Ruins of Alpha- Head to Azalea Town and go east into Union Cave. Go south up the steps and the ladder to your left. Surf over the water go north then west then south and then west once more where you will push a boulder and head outside. Jump off the first ledge and head into the building to the left. Go to the north side of the room (skip the hole) and interact with the middle tablet. Then walk counter clockwise around the room hitting each outside tile. Make a full round and a hole in the wall will open up, go inside and step on the white button.

Fusion Resort Penthouse- This is needed for the Creation Trio. After defeating Team Fusion at the Ruins of Alph, a drudge will have left behind a Penthouse Key. Bringing this to Fusion Resort on Serenity Isle, you can access the top floor via the elevator. Obtain the Adamant, Lustrous, and Griseous orbs there. After capturing them, you can go back to the legendary research center (west of Violet Town) and they will take the Orbs. This will give you needed space later for other orbs.

Dialga - After completing the Penthouse Sidequest, travel east of Chocco Town. When you get close to the correct spot, the Adamant Cave will open up, where you can battle Dialga.
Palkia - After completing the Penthouse Sidequest, travel to Spatial Sea. When you get close to the correct spot, the Lustrous Cave will open up, where you can battle Palkia.
Giratina - After completing the Penthouse Sidequest, travel to Haunted Seaway. When you get close to the correct spot, the Griseous Cave will open up, where you can battle Giratina.

Legendary Bird Trio : Articuno, Zapdos, and Moltres- Upon encountering Kyurem, Zekrom, and Reshiram, each will reveal a certain plume (even if you don't capture them). These plumes will enable you to battle Articuno, Zapdos, and Moltres, upon the plume being taken to their island and shown to them.
Articuno : Mt. Frozon (Iceplume from Kyurem required)
Zapdos : Mt. Dyno (Thunderplume from Zekrom required)
Moltres : Mt. Tritorch (Fireplume from Reshiram required)

Mewtwo- After defeating seven Gym Leaders in Johto, a Dragonite will approach you on Route 44, providing information on how to get to New Island, where Mewtwo can be found. Go to the dock in Olivine city, interact with the water, and use dive. You will end up on New Island. Go into the building and find Mewtwo at the end. You will find a team of pokemon that are the same as yours, but with moves they acquired through leveling up. After defeating them, Mewtwo will fight you himself, giving you the chance to capture him.

Mew- Once you beat the Elite Four of Tunod, return the top floor of Fusion Labs. You will find Mew there. Having an empty space in your party will allow Mew to join your team.

Lugia- Upon Lugia being released by Pius, a sailor will appear on Route 40, looking for someone with Dive. He will take you to the location of the sunken Whirl Islands, where Lugia will appear.

Ho-oh- After freeing Ho-Oh from Regina, it will appear on the Brass Tower's roof.

Celebi- After defeating the Johto Elite Four, you will find the Ilex Forest green and thriving once more. Interacting with the Ilex Shrine will cause Celebi to appear.

Legendary Titan Trio: Regirock, Regice, and Registeel- All are obtainable once you get the HM move Waterfall. Go into the entrance to Mt. Stratus from Geminite Village. By surfing in the water directly to your right after you enter the city's cave, you should be able to get to them.

Groudon- Unfortunately, the hardest one to get. After completing the Lance sidequest (See Heatran), Travel back to Mt. Silver from the Goldenrod Train Station. Battle Red, and if you defeat him, you will be given a Ruby. Take this to the first-floor chamber at the Embedded Tower to battle Groudon.

Kyogre- After completing the Ruins of Alph subquest, go to the basement of Slowpoke Well. Interacting with the tablet will cause you to fall to a lower floor, where a Sapphire will be found. Take this to the bottom level of the Embedded Tower to battle Kyogre.

Rayquaza- After completing the Ruins of Alph subquest, go into the Dragons Den. Interacting with the tablet will cause you to fall to a lower floor, where an Emerald can be found. Take this to the top level of the Embedded Tower to battle Rayquaza.

Jirachi- A snobby girl in one of the rooms at Fusion Resort will make you run many errands for her. Completing them all will give you a Wish Ticket, which can be taken to the right-most sailor in Oceanview City for a trip to Wish Island, where Jirachi will await the player.

Deoxys In the Peak of Alpha, type: NOT ALONE...
You can find the ... in the "others" section when you try to enter the message.. After typing this, go back to the start of the Peaks of Alpha and enter the other path. The room has expanded, and you can now go to the Undersea Grotto. At the end, you will reach Deoxys.

Uxie, Azelf, and Mesprit- At the uppermost peak of the Peaks of Alpha, a white stone stands. Interacting will let you visit one of three islands, each with a Legendary Pixie at them.(Note: You have to beat SOUL first)

Dialga- After completing the Penthouse Sidequest, travel east of Chocco Town. When you get close to the correct spot, the Adamant Cave will open up, where you can battle Dialga.

Palkia- After completing the Penthouse Sidequest, travel to Spatial Sea. When you get close to the correct spot, the Lustrous Cave will open up, where you can battle Palkia.

Heatran- After defeating the Johto Elite Four, travel to the peak of the Johto Victory Road. Lance will be standing at the tip of the mountain. Talk to him to initiate the Lance sidequest, and follow his instructions.

Regigigas- After defeating, fleeing from, or capturing the other Regis, approaching the central cave will cause it to open. Inside, you will find Regigigas.

Giratina- After completing the Penthouse Sidequest, travel to Haunted Seaway. When you get close to the correct spot, the Griseous Cave will open up, where you can battle Giratina.

Cresselia- Use Roar on the sleeping man outside of Violet City, on Route 31. Defeating him in a battle will net you a Lunar Wing. Bring this Lunar Wing to the Azure Inn, and the Innkeeper will give you a free room in return for it. Sleeping in this bed will bring you to the Dreamspace, where Cresselia can be fought.

Manaphy- Enter a surfing race in Evergreen Town. Getting first place will net you a Sea Jewel. Manaphy will then appear at the Spatial Sea and will dive into the water upon being seen. You will also need to bring a Pokemon that knows Rock Climb to reach Manaphy underwater.

Darkrai- After completing the Cresselia event, visit the VIP Villa in Palmtree Resort. Blake's Darkrai will take you to the Dreamspace. After a monologue, it will give you an egg containing a Darkrai. NOTE: If you don't have a free space in your party, this egg will be sent to the PC.

Shaymin- After defeating the Tunod E4, return to the Shrine in Espo Forest and type the code,: THANK YOU…You can find the ... in the "others" section when you try to enter the message. After typing this, an opening will appear in the forest. Once you enter, Shaymin will try to hide from you.

Cobalion, Terrakion, and Virizion- After they have shown themselves to you, a cave will be opened in the Darkwood Grotto. Upon entering, the three will begin to battle you. They fight you in a row without breaks in between, so be prepared.

Reshiram- After defeating the Tunod E4, The back area of Mt. Furnace becomes accessible. Reshiram can be found here.

Zekrom- After defeating the Tunod E4, The roof of the Oceanview Power Plant becomes accessible. Zekrom can be found here.

Kyurem- After defeating the Tunod E4, a secret area of Icicle Tunnel becomes accessible. Kyurem can be found here. Taking Kyurem to the Blackwhite Ruins inside of Mt. Mortar will allow you to change it's form to White or Black Kyurem. Note that this is not a perfect forme change; All that is preserved is level. Moves taught to it will be lost, EVs will be reset, and IVs will be randomized.

Keldeo- Go to Darkwood Town, at the right Wishing Pond, make a wish. The password is: JUSTICE!!! The cave between two ponds will open and you can battle Keldeo.

Arceus- Encounter every Legendary, and he will allow you to his cloud temple at the very peak of Mt. Stratus. The randomly-encountered ones (Latias, Latios, Raikou, Entei, Suicune) are not required.

Legendary Beast Trio: Entei, Raikou, and Suicune- After Regina captures Ho-Oh, travel to the top of the Bell Tower. Eusine will be there, and after some dialog, will leave. Either Entei, Raikou, or Suicune will be at the top of the Bell Tower next time you travel up it, and a random one will appear every time you climb the tower.

Victini (All Starters) (IS REQUIRED FOR ARCEUS) - Continue west of Seaspray Town to Soheal's Strait. Continue to Soheal's House, and defeat him in battle. The prize will be a Victini. By beating Soheal, you also unlock a new island! Mystery Island where you can get starter pokemon!

Latios and Latias- After beating the Elite Four of Tunod, they will begin to wander the Tunod region. They will change location daily, and won't disappear if you knock them out. Talking to Lars, the man inside of the Legendary Pokemon Research Lab outside of Violet City will give you a clue to their location.