The story begins in a rainy Andoria, following Siernan down a long hallway of murals of the original Heretic II (as the credits roll).  We learn that Siernan is either going mad or Morcalavin will return.  Obviously, the latter is the case (which is not to say Siernan isn't also going mad...)
The first playable map begins with the Ogle in Siernan's sanctuary, somewhere to the north.  The map is basically an extended cutscene where Siernan lays out the story as he sees it and his idea of how to take out Morcalavin (i.e., a mysterious time portal).  After the cutscene, you'll receive the Ring of Repulsion.  Then, unexpectedly, Morcalavin has appeared outside in the snow.  Don't bother trying to kill the seraph because he's invincible...just flee with Siernan through the portal.
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Siernan and the Ogle find themselves teleported to somewhere unknown, on a structure in a swamp-like area.
You must activate 4 switches and find one key before the story can move forward.  The first switch is embedded in a wall, and a good vault kick to the wall will make this switch triggerable.  The second switch is on the wall just prior to jumping into the water.  At the base of the waterfall is the key.  The third switch can be reached only after you activate the wooden platform from inside the structure; to get onto this platform, do a backwards-wall jump onto the protruding stone outside.  This action is performed by jumping toward the wall, and then pressing the down key (though if you have trouble doing this, don't feel bad to type the "kiwi" cheat into the console...this is the only place in the game where the backwards-wall jump is required).
The final switch is at the very top of the structure, reached by rope on the waterfall side.  Once all four switches are activated, Siernan will situate himself on the chained drop-door that is opened with the key.
After a cutscene where Siernan pieces together clues as to your location, the device in the center of the structure will activate, and you'll have to fight a handful of T'chekrik that come from a hive door outside.  Once they're defeated, talk to Siernan.  He'll tell you that he's unable to follow you, so you must continue on your own.
Once inside the hive, you'll immediately receive the Larva Spawner defensive spell.  If used near a Hive Mother, it will target her, and you can go inside her gut, and she'll pretty much poop you out to a level below her.  After some exploring and taking out bugs, you'll find that by going through one of the Hive Mothers you receive the T'chekrik Hellstaff.  It's a weak weapon, but essential to kill T'chekrik from afar, several of which you'll have to kill as soon as you acquire it.
One door in the main room leads to a set of caverns, protected by female T'chekrik.  Since they're static, you can either kill them or avoid their attacks until you reach a stone door that hasn't been opened in centuries.  Shoot at this door until it activates, and go down the long, dark, scary hallway, receiving the Light of the Seraph shrine.  This room is one that makes you aware of the complexity of your circumstances, as you discover a crystal and a map of Parthoris, and a ladder leading to a large lever.  This lever is activated by first crouching and rolling into it, then pushing it thrice (which will require you to jump onto its edge to be heavy enough).
Once it's activated, and you go to the base of the ladder, the device in the center of the room comes to life, and an extended cutscene follows.  The High Priestess is pissed at Siernan for activating her "Time Beacon" and she thinks he's crazy when he says it's to stop Morcalavin.  You learn that the beacon is actually the first of three.  The other two are in Fairbury and Vendia, which open a time portal at the World's End Mountains.  This cutscene lays out heretofore untold history of Parthoris, which takes even ancient Siernan by surprise (since the Andorians are known for their record keeping).
To get out of the room with the crystal, return to the dark hallway and to the left of the stone door is a button.  You must shoot it from afar, because if you press it, the door will crush you.  Return to Siernan after learning that the priestess is banishing the two of you to this hive forever because of the danger you now pose to history.  His logical self tells you how you can and how you must escape to activate the other two beacons.  Thus, you must leave Siernan and venture even further into the hive.
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Cliffs of X'chekrik
At the start of the map, you receive the Blade Shrine.  If you retrigger the mechanism that houses the shrine, you'll discover a pool of water that leads to the other side of a gate, where there's a switch to open that gate.  Do this now so you don't have to later.
The main hallway has a locked door and leads to a huge upright cylinder on the edge of a cliff.  You won't be able to explore this area until you kill off droves of T'chekrik. Eventually, you'll reach a pillared room that has three options.  The first option will be closed off to you as you approach it, the second option is a waterway, and the third option leads you upwards, back to the cylinder.  The fastest route is to take the waterway first.  Where the giant spider is, a dropdown route leads to an Amulet of X'chekrik. If you continue along the waterway, you'll find a floor button that opens a secondary gate at the beginning of the map for 45 seconds.  You cannot make the return journey in that time frame, yet.
Now take the cylinder route, whereby you'll activate the cylinder (which rotates).  A stone platform is attached to the cylinder, revolving with it, and if you jump upon this, you'll go around the cliff's edge and reach a rope that leads you into the cylinder.  A T'chekrik will shoot at you, and you can shoot at him, but most of your attacks won't hit each other because of the cylinder's rotation (this is interesting to see and wasn't planned when I built the map).  At the center of the cylinder is a key.  Once you grab the key, you'll have no choice but to drop into some water below.  Once, you get out of the cylinder, you must crouch to avoid the revolving stone platform.
With the key, open the door in the main hallway.  In the small room are two busts that require amulets.  The first amulet opens a door into the pillared room, thereby creating a route that grants you the ability to reach that secondary gate in 45 seconds time.
Beyond the gate is a room of spiders, wherein you'll receive the Grappling Iron.  This device substantially increases the Ogle's mobility.  One tunnel upwards leads to a button that opens a gate for 20 seconds.  I suggest you practice with the grapple in this tunnel, because if you make a mistake you'll only fall in water.  Note that the grapple won't easily pull you out of water.  Anyway, the 20-second gate is unreachable at the moment.
Instead, take the tunnel that leads downwards to the underbelly of the mountain (a route that heretofore didn't seem like a route).  You'll need to kill or avoid upside-down T'chekrik to reach the tunnel on the opposite side.  This tunnel leads to a button that opens a gate that allows you to...well, reach that other button that allows to you open that other gate (the one that is open for only 20 seconds, pushing you to use that grappling hook like nobody's business).  Eventually, you reach the cylinder again.  A note of caution here:  the grapple cannot latch onto moving objects, doors, or other entities.  So you must wait for another revolving platform that takes you to a ledge on the other side of the cylinder.  This ledge takes you higher still, so that you may return into the cylinder.  At the top-center of the cylinder is the second amulet, which you can reach with your grapple.
After getting back safely to the ground, return to the small room and place the second amulet around the second bust.  A path will open up, which isn't what it seems. Let's just say you wind up in a cavern with two doors (one locked) and some power-ups.  When you're ready at full health and full armor, face the horde of T'chekrik that rain down upon you.  This new area is the last main area of the map, which houses an embedded octagonal room.  You may open the door that returns to the pillared room, but this is just for effect.  To get into the octagonal room, follow the cliff's edge and use your grapple.  Drop through the ceiling and defeat the giant T'chekrik female.
After you pick up the X'chekrik idol and try to use it on a pillar, the High Priestess will shield the room and taunt you.  Items and health spawn during your battle with her.  There is a limit to these items, so don't be wasteful.
After you defeat the priestess, she tells you that she has already warned the Fairburians about your intentions (although you might piece together that she hasn't told them everything...the beacon).  She mentions that Corvus is waiting for you, a bit of foreshadowing.
Use the idol on the pillar quickly (unless for fun, you wish to take out all the appeared T'chekrik). You'll drop down into a cavern with a key that opens a door in that other cavern (you'll be lead back to the locked door).  After a cutscene where the priestess pleads with you to change your mind, you teleport across the continent to Fairbury.
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Fairbury is a much-needed change of scenery.  You find that long ago the Fairburians (a city of elves) placed a gruesome warning to the T'chekrik to stay away.  This might explain why the T'chekrik are so xenophobic and uninvolved in the affairs of Parthoris (other than the priestess, who we found out earlier, was given secret responsibility by the exiting seraphs).  Use your grapple to launch yourself over this warning.  Pick up the Hydrospray spell.  Go down a crevice and find yourself behind a waterfall.  Jump through the waterfall and swim your way to a huge wall that is actually a dam.  The dam has three drains, and the left drain houses a locked door that cannot yet be opened.  You will likely need your grapple to safely traverse these drains, though there isn't any reason to venture into them.
A nearby cave leads to an elf who freaks out when he sees you.  The elf runs to tell an elf-guard (who is talking to a Ssithra and his injured mate) and then runs further to tell others.  The elf-guard comes to find you.  (Inside the cave is a door that is chained; this door is not passable until much later.)
Outside the cave, you'll find a route to Andoria/Silverspring (for effect) and a metal gate that's been recently closed to prevent your passage.  Behind an upright two-wheeled wagon (not sure what to call it!), is a Reservoir Key that opens that locked door back at the dam.  Oh, and by the way, if you don't attack the Ssithra, he won't attack you.  In fact, all the Ssithra in Fairbury are peaceful until you invade their space or news reaches that you've killed their kind.
After opening the reservoir door at the dam, you'll find yourself in a room with a mana shrine.  The only exit from this room is a breakable gate on the ceiling.
Atop the dam, you'll fight off a number of elves, one of whom is invisible.  If you ever wondered the technical limits of Heretic II, well, the view from atop the dam will show you.  I didn't give the view much detail, because the next fight sequence pushes the entity limits.  In a corner, you'll find several health potions; as soon as you grab a potion, two mutant Ssithra make their way to the top of the dam via gondolas shooting a barrage of exploding arrows at you.  These mutants cannot be killed by magic or weapons -- well, they can, but you don't have enough.  Once they reach the dam, you must kick them off the edge!  Once both have reached their watery graves, the Key to the Eastern Gate appears.
Return to the metal gate, go across the long bridge, receiving the Firewall along the way.  Kill the elf-guards who are there to stop you from entering the city.
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Fairbury Proper 1
As soon as you enter Fairbury, be prepared to fight off several elf-guards.  You will also see some Ssithra in a soup line who are peaceful until they get drawn into the battle, so if you can, keep them peaceful.  When the common grounds are safe, do some exploring.  Eventually, you'll find that even though there are lots of places one could go, everything has been locked down because you're in town.  Your only option is to break through a window at the top of the grassy area that holds the line of trees.
Inside the building are Ssithra determined to kill you.  You will wind around, past a Ssithra statue and into a cave, and given the close quarters of this section the city-dwellers have the advantage.  Once in the cave there are two buttons:  the first opens a door leading back outside, and the second opens a door leading downwards.  Ssithra are waiting for you beyond the second door, but some exploding barrels are also present, dangerous for both you and them.  An elevator takes you into a warehouse.
The warehouse is littered with elves along a conveyor belt.  This section is rather straightforward, and you'll reach a larger warehouse room in which a cutscene plays where Arthur from The Heretic Fortress and two guards (a warrior and a cleric) are with a tour guide -- this scene is dedicated to all my THF buds!  You face a horde of elves afterwards, and then you'll try to open some doors (one is locked).  After you try to open the door opposite the locked door, a bunch of crates will roll over, revealing more angry elves.  A duplicate Warehouse Key will be discovered, which opens the locked door.
Inside this room is a complicated-looking warehouse map.  Basically, make sure you open all the doors (South Main, Weapons Room and City Wall). The left switch determines which door you'll open or close, and the right switch actually opens or closes it.  The North Main door is doubly-bolted (so it can't open), and the "East Control Room" door is the room you're presently in, so obviously keep it open.  The camera will show you when you've opened a door, and the map will show you whether a door is open or not.
Past the South Main door are more crates, leading to an exploding barrel that reveals a Ssithra Shield. In the Weapons Room is the Phoenix Bow.  Back in the cave, the Fairburians have placed a deadly device that they hope will catch you off-guard, and chances are it will, once.  Roll beneath its line of fire.  Use the Ssithra shield on the Ssithra statue and eventually you'll make your way back to the City Wall outside (after passing through some aesthetically-pleasing rooms).
Past the City Wall door you will go along the edge of the city.  The rest of the map is straightforward, and I hope you enjoy the atmosphere of this section.
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Fairbury Proper 2
You're in a flowing sewer, and must grab a ledge before you fall to your death.  After you climb the ladder and activate the turn-switch, the room will fill with water (and there is air trapped beneath the crate, which floats to the ceiling). After some time, you'll hear a breaking-sound which reveals three shootable buttons.  Shoot all three to open a door at the base of the ladder.  As quickly as you can, get to the Lungs of the Ssithra shrine.  The two Ssithra in this section are annoying, but don't let them slow you down.  Follow the path upward and press the button that opens the gate.
You'll find yourself in a small storage room.  Nearly if not all the barrels in this room have items.  Receive the Fire Blade Shrine, too.  A statue of Corvus is in the storage room (and you may understand this symbolically however you wish). The statue is pushable, so push it into the water; it will sink down and destroy the sewer fan.  Swim past the fan and reach a stone room, where you'll have to kill some Ssithra as soon as you surface.
Outside this room is a narrow canyon that is heavily guarded because the Fairburians know that you've taken this route and they're trying to bottleneck you.  Once you reach the chicken coup, and if you're in need of health, there's some vials behind the shed.  Before you can get back into the city, you must drop into the water and push a button to open a gate.  Since you will be standing in flowing water, you must use your grapple to steady yourself so that you can push the button.
Back inside the city, your route is straightforward.  A switch will open a door, and a vent above can be broken.  If you follow the vent, you will be lead to a cutscene in which you eavesdrop on Corvus and a Fairbury city official.  You will accidentally fall into this conversation and be knocked unconscious by a mutant Ssithra guard.  Given the murders you've committed thus far, Corvus will let the Fairburians imprison you and take all your weapons.  Because the Tomes of Power are missing, and because the Fairburians mistakenly believe the Ogles are the culprits (because of your havoc), Corvus must journey to your homeland to find answers.
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Ogle Vigilante (2)
The Ogle wakes in a cell with nothing but his staff and knives.  If you break the chains holding up the stone bench, a crack in the wall will appear.  If you throw knives at this crack, the wall will crack up to the ceiling until the ceiling itself caves in.  Climb into the cell above you, and on the wall is another crack that breaks into the cell adjacent.  This cell is a torture room.  A dying Ssithra offers you a key.
If you look out the door, there are two buttons.  The left button opens the cell door.  The right button makes the metal floor drop into lava (so if you're a bad aim, stay on the stone step!).
Once you're out of the cell and try to leave the prison, a Caurthorian will spawn.  He cannot be killed except by the lava in the torture room, so you must fool him into the cell and press the button that drops the floor ASAP (before he teleports himself out -- might take a few tries).  Once he's dead, you can escape the prison.
Some of your weapons (Phoenix Bow, T'chekrik Hellstaff and Ring of Repulsion) are locked behind a gate, alongside a Triangle Aura Device; the gate can be opened by a nearby floor lever.  Climb the stairs, kill some guards, and you'll find that you're back at the long bridge across from the dam.  Journey back to that cave with the chained door and use the key the dying Ssithra gave you.
The second beacon is finally revealed!  Climb through the bottom and pull a switch on top.  The beacon will expand upwards toward the sky, and you must climb higher to reach another switch.  Pull this switch and the beacon will activate.  The voice of Morcalavin will taunt you, and you'll immediately find two mutant Ssithra are shooting at you from below.  If you jump to escape (since you really have no choice), you'll teleport to who knows where right before you hit the ground.  Morcalavin snickers, as his return is 2/3 complete.
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You've been teleported to Vendia, and if you read the Ogle's journal at this point, you'll find the poor creature is utterly confused but refuses to be Morcalavin's pawn.  Yet, he has no choice but to continue on since this quest has put his own people in danger. Vendia is the northern seraph ruins, and the specific part of Vendia you've been teleported to, high in the mountains, houses the third and final beacon.
The first room can be perplexing.  Another Grappling Iron is amidst some gorgons munching on a cadavar.  Each corner of the room has a button that if you push in the wrong order will spawn an angry gorgon in the center of the room.  Above you are a Blade Shrine, a Fire Blade Shrine and a Blue Crystal.  Above you is also a button that when you push it lights the torch next to it.  This button is the first button to push (one torch).  The buttons below must be pushed in the order of the torches on the wall next to them (two torches, three torches, four torches, five torches).  If you push a button out of order, all lit torches will unlight and you must start the sequence over, beginning with the torch above (not to mention, an angry gorgon will spawn).  Once, the fifth button is pushed, an exit will appear and you'll have to kill an incoming cyclops.
You'll enter the main hallway, which has frozen cyclops that come to life at various points.  To the left is a bright waterfall and a dark pit.  In the middle is a gateway leading to the snowy outdoors.  At this gateway, you can place the blue crystal along with the other two crystals you receive later (once all three are placed, the gate opens and the final cyclops will awaken).  At the end of the hall is a room designed like the initial room (minus the buttons).
Traverse the pit with your grapple.  You'll end up in a room where have to fight a Cauthorian, and then you must grapple upwards outside through the snow to locate the Violet Crystal, which is behind the harpy's nest.  Once you have the crystal, backtrack to the main hallway.
The room at the end of the hall holds the Green Crystal.  On the ledges above are ammo and silver armor.  As soon as you grab the crystal, you'll battle a giant gorgon.  Since it moves quickly and can kill you quickly, I suggest you grapple to a nearby wall and take it out with your phoenix bow.
Once you place all three crystals, and you're on the walkway outside, you'll receive the Sunsphere spell.  Climbing the ropes will lead to a button that opens the large swinging doors.  Let the gorgons jump to their death, leaving red splatters in the white snow.  Enter the darkness.
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The Last Beacon
You will grapple across three dark pits, facing gorgons, harpies and a cyclops.  Then you will attach your grapple to the line above the muck (because the surrounding walls can't be grappled).  On the other side of the muck, you'll find a chained door, and experience should tell that you behind that door is a beacon.
Outside on a breezeway are a couple of cyclopes.  At the end of the breezeway is a stone door that, at first appearances, may not seem like a door.  Above the breezeway (which you can only reach by grapple) is a Caurthorian that will spawn, the mouth of dragon holding a key, and a button that opens the stone door.  Beyond the stone door is a dark hallway similar to the long hallway in the Unexplored Territory -- one that ends with a Light of the Seraph shrine.  Grab this shrine, and a dozen tiny spiders will attack you.  On the ceiling in the hallway is a passage.  This passage will lead you to a Silver Bar.  Once you grab the bar, be prepared to face two Cauthorians once you return to the breezeway.
Use the key to unlock the chained door.  What comes next (or should I say who comes next) I won't mention here, but just know that you need the silver bar to finish this section and the map.
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The Return of Morcalavin
With all three beacons activated, you are now at the World's End Mountains and ready to enter the time portal.  First, you must break three crystals in the initial lava-based area.  The first crystal is under the bridge in the room with the two doors, and the other two crystals are beneath the rock walkway in first room (don't grapple too close to the lava or you might fall in!).  After you break the crystals and load up on phoenix arrows, pull the two switches, kill the gorgons and head down the stairway until you reach the rainy outdoor arena.
Jump over the surrounding lava and onto the arena.  There are three book shrines: gold armor, healing and mana.  Choose the two you need most, because before you can grab the third, the High Priestess will shield it and make a final attempt to stop you.  Note that your grapple will not latch onto anywhere in this section.
After you defeat the priestess, she will open three portals and T'chekrik males will attack you nonstop.  Three more spawn when a certain one is killed, so try to avoid killing them to avoid more spawning.  After 30 seconds or so, the defeated priestess drops the force-field on the third book shrine, and as soon as you grab that shrine, the three statues in the middle of the arena come to life, and they're very fast-moving.  The statues will kill the T'chekrik if provoked, and will certainly kill you, too.  To kill the statues, you must trick them into falling into the lava.  Once the statues are dead, a mountain will rise through the arena.  Climb this mountain, and at the top, use your grapple to latch onto some attached wood to pull yourself onto the overarching stone structure:
An extended cutscene follows, as we go back into the past and watch Morcalavin escape from the moment he should have ascended in the original game, leaving Corvus baffled.  In present day, Morcalavin renders the Ogle unconscious and flies off to destroy the Beacons of Time and to collect the Tomes of Power to revive his plague.  The High Priestess rescues the Ogle as the arena is in structural collapse.
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The Parthoris Sanctum
You awaken and the priestess updates you.  You teleport to a sanctum where Morcalavin is waiting for you.  Among other things (to bring various plot threads together), he tells you that he's ready to take your Tome from you.  Thus begins the final battle.
First knock the plague spreader into the bottomless pit that surrounds the elevated platform (it's not really bottomless, but very deep, and will kill anything that falls into it).  When it dies, the force field will go down and you can grab a Tome of Power.  Place the tome on a pedestal on the elevated platform.
Spreaders will spawn, and once they're killed you can grab a second Tome.  As soon as you place it, you must fight more spreaders on the platform.  Once they're dead you can grab a third Tome; placing this Tome will cause two cyclops to spawn on the platform.  Once they're dead, you can pick up the fourth Tome.
Placing the fourth Tome will cause Morcalavin to taunt you, and as soon as you grab the fifth Tome, he will place a force-field around the elevated platform to prevent you from placing the Tome.  You must wage a lengthy battle against him, similar to the original game, except that the room dynamics are different.  To draw Morcalavin away from the elevated platform, hide behind a pillar, because otherwise he will stay up there and throw magic at you from all the way across the sanctum.
After you drain his life, the small field that protects the button will go down, so try to get a final shot when you're near that small field; otherwise you'll have to drain him again and again and there are only so many phoenix arrows.  When you push the button, a Teleport of the Gods spell will spawn where the Tomes had been.  Draw Morcalavin away from the elevated platform before you teleport, otherwise he is liable to kill you before you can even place the Tome.  After you place the Tome, a sixth Tome will spawn, which is your Tome, and place it on one of the two remaining pedestals.  Even if Mork knocks you out in the few seconds that follow, you will witness the end of the game cutscene extravaganza.
It begins with Mork belittling you:  "Foolish Ogle!  The last Tome is my false Tome!"  Yet, who do we know that also carries a Tome?
After the cutscene is an epilogue cutscene, so stay tuned.
By no means has the story of Parthoris come to an end, but Morcalavin is gone, once and for all.
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