Since the Elona+ mod doesn't have an English translation in-game of most of the things that go on here, much of it is just an outline on how to proceed. Since it takes a while to get to this part of the game, more details need to be filled in. The time that you receive some of the rewards may be off.
The Main Quest
Once the Elona quest is done, you will appear on the world map at Port Kapul in North Tyris, having spent 3 years away while the ether forests regrew after being destroyed in the storyline of Elona. To begin the next quest, you have to head to South Tyris. This begins by walking or warping to the North Tyris south border town that is south of the Ancient Castle and Doujou. Talking to the Caravan master there before this would give you the option to try to go to South Tyris, but it wouldn't work yet. Since you're done in with the quest, now he will turn a blind eye to you sneaking on. You are taken to South Tyris now, and you start on top of the South Tyris North Border town. To go back to North Tyris, you have to enter this town and talk to the Caravan master there again. You cannot use the return spell to go back to any North Tyris location. It is important to enter this town now, so you have a location you can return to, since they are very rare in this part of the game.
Note: The current translation has you select "Observe caravan" to transition between North and South Tyris.
Obtaining the Key Card
Go to Melugas and talk to <Heinrich> the iron carnel to the left of the north entrance. He will allow you rights to talk to Doctor <Gavela> about obtaining a "Key Card". He will request you to go obtain three quest items from three different dungeons; in exchange for the pass into the main dungeon Rehmido.
After collecting all three quest items, return to Doctor <Gavela>. He will give you the key card, and the Statue of Mani as a bonus.
The first trip into Rehmido
Rehmido is just down the small road that connects to Melugas. The dungeon itself is actually totally random except for the last floor and one floor in the middle. At 7th floor, you will end up fighting a <Mobile Communication Equipment>, presumably run by the doctor. There are also several mechanical enemies with it, including Xeren electric tanks and Xeren satelite units. After you clear this, you find that the way down is blocked. Return to the doctor for a reward. He will also give you a key to proceed.
The second trip into Rehmido
At 15th floor, you will run into <Orphe> the chaos follower and the <Chaos Unicorn>. After defeating them, you can proceed downward. At 23th floor you will meet <Mobile Communication Equipment> again (drops the same card and figurine), but this time it would be neutral. The door on this floor is locked. Return to the doctor now, and he will give you a reward including 3 forbidden meats. He will also allow you to proceed to the final floor now.
The third trip into Rehmido
Make your way down again. This time you can make it all the way down to the 30th and final floor. You will end up in a fight with the <Meshera plant> and several Infected yerles soldiers. No matter how many time you kill the plant, you will be unable to keep it from respawning. You will receive a message to retreat, so do so. The floor does not allow teleportation, so go up the stairs you came in from to use Return. Return to the doctor, who will give you a quest item in order to get the ether material you'll need to kill the plant.
The Mountain Pass
To proceed, you need to head to the Ancient Garden, by going through Mountain Pass. Once you arrive in the Ancient Garden, an alarm will sound. This is the same as an alarm when you force your way into a Guild, so you can use Incognito if you wish. Keep in mind that the ether corruption is still in effect here. There are many neutral Old humankinds in the town, but they neither talk or do anything else of use. There is not much here at all. Your objective is the <Ether Generator>, located at the top of the town. If you have incognito, you can "speak" with it, to obtain the item you need. Killing it also completes this portion of the quest, along with giving you its card and statue. Return to the doctor, who will take the fragment of crystal ether and turn it into the [Ether Blaster]. You are now ready to finish the quest.
The Final Battle
You can warp right back to the 30th floor in Rehmido. You can kill the plant off for good now. However, once it is killed, the message "something shot out of the flesh cake!" appears, and you encounter the final boss, <Meshera Alpha> the deformed angel. Any remaining infected soldiers will regain their senses, and try to help you fight the boss. After it is defeated, you get the victory message.
The Beginning of Act 3
Once you return to the South Tyris world map, you get the "3 years have passed" message, and are automatically at Melugas. To continue the story, you need to return to Palmia and speak to <Erystia> the scholar of history. She will give you an option. If you accept, you have to talk to her again to receive a letter, which you then have to take to the captain near the docks at Port Kapul.
You will arrive in Ulm-Leson, but once you try to leave, you will be picked up by Doctor <Gavela> and whisked back to South Tyris. To get back to Lost Irva, you first need to meet with the doctor in Melugas, then meet him again in the Ancient Garden near the stairs to the mountain pass. He will be waiting there as <Melugast type0> the dimension driver. This is your first warp point to return to Lost Irva. After accepting his ride back, he will wait at Ulm-Leson when you want to return to South Tyris. If you return, you will be dumped on the world map near Ludus. However, it is not necessary to return yet if you want to continue the quest.
First trip into the Cradle of Chaos
To continue, you will next need to head to the Cradle of Chaos, which is located in the very center of the continent. Before entering, you must speak with <Sophia> in the Sacred Library of Irva. The Cradle is the main dungeon of this act, and you will be able to use a Return spell or scroll to go back to the lowest floor you reach. Your destination is the 4th floor, where you will speak with <Marka> the silver bear.
The return to Palmia
At this point, you cannot continue downward, so exit the dungeon using your preferred method, and go back to Ulm-Leson to get a ride back to South Tyris. You'll need to use the caravan to get back to Palmia from here, and then speak to <Erystia> again. Doing so will allow you to proceed further into the Cradle. You are also rewarded with the <Asteroid Belt>, 5 platinum coins, 5 card packs, 5 small medals and 500 music tickets.
Unfortunately, you will need to get back to Lost Irva at this point by returning to the Ancient Garden and getting a ride back with Doctor <Gavela>.
Second trip into the Cradle of Chaos
Upon returning to the 4th floor, you will now be able to proceed downward. Your next goal is the 7th floor, which is a unique area where you will encounter <Aikage> the sinobi mask and a large number of his minions. When you defeat him, you will still not be able to proceed downward, and will need to exit again. However, upon leaving the dungeon, <Norne> the guide will appear, and take you to the Shrine of Guardian.
The Shrine is a small map that you pass on your way to the Cradle. Speaking to <Norne> in this area will now allow you to teleport back to Larna in North Tyris, speeding up your return to the main continent greatly. You can also return to Lost Irva by speaking to <Norne> in the northeastern corner of Larna.
Island in madness
To break the barrier on the stairs in the Cradle, you will have to return to South Tyris and visit Valm. Talk to <Leiki> near the beach to get three options. Choosing the second one will warp you to the bottom of a map called the "Island in madness". To complete the map, you have to defeat <Nine Head Dragon> the abyss at the top of the map after getting past his minions. Talking to the <Abyss Princess> near the start will allow you to return to Valm if you need to.
Until the boss is defeated, the map will randomly raise your sanity level with the message, "Horrible call rang in your head". The amount of sanity this costs you seems to rise the closer you get to Nine Heads. Normally, this would not be that tough to deal with, but when your sanity is raised to a certain level, you will be kicked out of the map with the message, "Your mind cannot stand any more".
The middle part of the map contains many jellyfish kraken, and many more tsathoggua surround Nine Heads. Since teleporting is allowed on the map, you could potentially skip the kraken, but the yith spamming eye of insanity will still cause a major problem because of the map restriction. The map can potentially be tough to clear without lowering your sanity somehow, so bringing along something that can reduce sanity described here, or using an evolved little girl or other pet with the rain of sanity special action really helps.
After defeating the boss, you can either use an escape scroll or talk to the <Abyss Princess> to leave. The death of the dragon unseals the stairs on the 7th floor of the Cradle. However, if you return to the Deep-sea castle and talk to the princess, she will give you a free abyss lunch. When eaten, it restores some sanity, gives 15 turns of regeneration, and 15 turns of the Super Regene special action. She will also randomly give another one when given small medals, although it is more likely you will get her other lunches. To get the option, cancel out of her conversation options, which appear to be unusable in the English version of the game.
Following the defeat of Nine Heads, <Erystia> in Palmia will have new information for you. She will give you four conversation options. These options are quests that will become available once you accept them. The NPCs that take you to quest maps will not appear until you select the corresponding option.
New Test Site
Selecting the first option will cause <Regulus> the altered to appear in the inn inside of the North Tyris South Border town. Talking to him and selecting the second option will bring you to the New Test Site, which is accompanied by violent sound effects. Upon entering the map, you and your pets will lose a large fraction of health and natural health regeneration will be disabled. Healing spells and regeneration buffs will still work, however. <Regulus> will accompany you as neutral help. While on the map, you will randomly take nerve damage with it's additional paralysis effect with the message, "Nerve gas has been floating around!".
The map itself is fairly small, and is filled with many meshera beta and testers. The testers are in small jail cells, so you must either use attacks from a distance or bypass the barrier in front of them in another manner. Once all the enemies on the map are defeated, your journal will be updated. You can then leave the map via the stairs or other desired method.
Afterwards, head back to Palmia. <Erystia> will reward you with an astral light pen, 2 scrolls of gain attribute (to be used for the new artifact fusion with <Irma> the indomitable smith), 3 jewels of brilliant diamond, and 20,000 music tickets.
Castle of Ice
Selecting the second option will cause <Marka> the silver bear to appear in Noyel's church. Talking to her and selecting the 2nd option will warp you to the Castle of Ice. <Marka> will accompany you for this mission as neutral help. The exit is a downward set of stairs near where you entered the map. Like the New Test Site, you will also lose a large fraction of health entering or loading into the map. It is snowing here, and the map itself might cause the Chills status effect.
The map is packed with chaos spirits, chaos paladins, chaos hunters and chaos shamans. Your target is <Lazasye> the destroy, who is near the top of the map. The chills effect will likely make its ice ball attack much more dangerous. After its defeat, you can exit from the stairs or with an escape spell.
Selecting the third option will cause <Shuraida> the expert merc to appear on the second floor of the Dock. Talking to him and selecting the 2nd option will warp you to the Ruined City. <Shuraida> and his mercenaries will accompany you for this mission as neutral help. The exit is a downward set of stairs under a well near where you entered the map. Unlike the New Test Site and Castle of Ice, you will not lose any health upon entering. The map randomly causes the bleed status to the player and all friendly characters.
The map starts you with <Shuraida> and his mercs (level 130) near you with the northern part of the city filled with a large number of zombies, necro dolls, liches, and a few crying witches (all level 140). Your target is <Roatonis> the infections, who is near the top right of the map in a ruined church along with his guards.
Selecting the forth option will cause <Raizel> the old wizard to give out his quest located at the Eulderna blimp. Talking to him and selecting the 2nd option will warp you to the Eulderna City. <Raizel> will accompany you for this mission as neutral help and several neutral high-magicians and a few palace magicians can be found in the map fighting the enemies. The exit is an upward set of stairs near where you entered the map. Like the Ruined city, you will take no damage upon entering the map. The map will sometimes announce the message, "Rebel magicians were fueled by revenge." which increases the special gauge of all enemy magic archers and eulderna summonknights in the map.
The map has a large number of chaos spirits, chaos paladins, chaos hunters, chaos shamans, eulderna summonknights, and magic archers. Your target is <Inqtual> the revenge, who is located to the bottom right of the map.
Third trip into the Cradle of Chaos
After completing the 4 side quests, traveling to Melugas to talk to Doctor <Gavela> will cause him to give you a new journal item. You can return to to the 7th floor and will now be able to proceed downward. Your next goal is the 10th floor, which is a unique area where you will encounter <Egelveil> the bind. In the fight against <Egelveil>, 4 Melugast typeMs will aid you.
You will not be able to continue your descent after defeating <Egelveil>, so return to Doctor <Gavela> to finish the quest. He will reward you with the <Mighty Arms>, 2 Scrolls of Gain Attribute, a Spirit Cloth Material kit and a mind disc.
Fourth trip into the Cradle of Chaos
Starting floor 12, various neutral NPCs can be found who possess special weapons every two floors or so.
The 15th floor, named "Hall", is a special area with no enemies. Instead, you will encounter <Belphat> the cosmic sword and <Norne> the guide, the latter of which will prevent you from going further. If you have space for an additional ally, you can ask <Belphat> to accompany you—despite this, he isn't a "true" pet, so things like the the Call Familiar special action won't work. Speak with <Norne> to proceed.
At this point, you can continue downward with <Belphat> in tow, or you can reunite him with his long-lost friend for a reward. If you bring <Belphat> to the Dock and speak with <Kuroya> the looking universe, he will give you the <Amulet of Yekub>, 2 yith-yakis, and 3 hot and gorgeous gifts.
On the 16th floor, <Saimef> the dogged will give you a god heart if spoken to. When floor 20 is reached, no further progress can be made without a key, which you can either buy packaged with "recovery item assortment" or "maintenance assortment" for 99999 gp, from <Manytia> the adventure merchant, the NPC in the room.
In floor 25, <Lankata> the lightning of blue will offer the player 4 untranslated answer choices before the player is surrounded by zanan old soldiers, lothrian agents, and zanan enhanced soldiers. Every couple of turns in this floor, will cause the soldier's morale to go up. <Lankata> the lightning of blue is the target. Once <Lankata> is finished, you will receive a rusted bell. You can also skip this fight by rushing to the staircase. If <Lankata> lives it changes an event later.
In floor 30, <Aikage> the sinobi mask will talk to the player giving 3 untranslated answer choices. The room will be filled with necro dolls, an <unitdead-jack>, <unitdead-queen>, <unitdead-king> and <unitdead-joker>. You can also skip this fight by rushing the staircase.
Proceeding to floor 34, <Alfred> the cangnan wind can be spoken to, when this is done, he will proceed to shatter into bits and bobs leaving behind an axe, the <Guliwelzen>. This event changes depending on the previous 2 choices. Leaving <Lankata> alive and killing the unit-dead allows you to save him by (b)ashing him awake.
In floor 36, <Aile> the attendant will be there, then in floor 38 <Vessel> the white hawk will be here, then finally in floor 39 the player will find Black gauntlet <Leold> here he will give untranslated dialog, then talking to him again will give the player the option "I will fight Tezcatlipoca" choosing that will initiate the fight with <Tezcatlipoca>.
After you beat him and finish talking with <Leold> again, you will have to go and talk to <Sophia> in the Sacred Library of Irva, all the dialog is currently untranslated pick any option to get the yellow gem stone of Heart of twilight, return to the cradle of chaos and talk to <Leold> once again, then choose <i will go to God's prison> to fight <Enthumesis>. <Leold> will be with you during this fight, but no god-related effects work in here (Wishing, pray etc...)
Once you defeat <Enthumesis>, there will be no time to rest. A strengthened <The Chaos Child> will spawn. Unsure if it's actually dangerous, but put on contingency and speed (which might still be active anyway) and run around until another NPC spawns. You can assuredly safely collect your spoils then. Keep passing turns until you're teleported out.
To Aimwell, West Raskilis valley, and the final battle
At this point, talk to <Norne>. Return to North Tyris, then go to Vernis. Norne should speak with you there and give you a (quest) item. Then, talk with <Loyter> in the bar. This teleports you to Aimwell, and you'll be right on top of Zaile. (If you wish to get out of Aimwell, talk with Loyter in the cemetary area, south center of Zaile).
There is not much to do on this continent, but exploring shouldn't take too much time regardless. Your goal is to simply "climb" to floor 9 of West Raskilis valley, which is the nearest location to Zaile.
Once you are there, talk to <Mikraanesis>. Talking to her a 2nd time and choosing the 2nd option will teleport you back to the overworld and give you 2 other items.
Either way, head back to Cradle of Chaos floor 39 and talk to Leold there. You'll have to fight Orphe the chaos disciple first, but you'll have strong help. Do not worry about <The Chaos Child> there; he won't attack.
When Orphe is down, it's then a fight against <Jaldabaoth> The Chaos Child. This shouldn't be too hard after <Enthumesis>. The main thing to keep in mind is it's very eventful and nonstandard.
And that's it for the main story, with act 3 officially completed. Upon exit of the area, another 3 years will pass.
You can talk with Leold on floor 39 again for a slight progress number boost in your journal, but this doesn't seem to affect anything. You can also talk with <Sophia> to get additional precious items now (in version 2.05 on). Plus, life and speed increases via AP are no longer capped.