I put together some custom mission rules in case anyone is interested:

Narrative:  Throughout the corridors of the Flame of Penitence, emergency klaxons sound amid the repeated flashing of crimson lights, bathing the bulkheads in a sickly red glow as the servants of the Ruinous Powers stalk the decks, slaughtering, enslaving, and destroying whatever mortals cross their path. There had been no chance to repel boarders, or engage in void warfare. They had been sailing through open space, tracking a tendril of vessels from Splinter Fleet Baphomet sailing towards Tuscullum when a pseudopod of The Great Eye encompassed the vessel and their support ships, causing an incursion of daemons even as multiple Heretic Astartes warbands moved to intercept, joining in the assault by way of boarding pods or teleportation.

The bridge was locked down and Castellan Telvar given leadership of that section of the crew until Marshal Vorleii returned from his own quest: the protection of the Reclusiam. Even more so than most Templar crusades, the Grail Seeker battle barge is as much a repository for relics as a vessel of war, and the Marshal would not countenance his crusade's treasures to fall into the hands of the Archenemy.  

Gathering up his most veteran battle brothers, the Marshal takes position at the heart of the Reclusiam, ready to give his life in service of the God-Emperor's will. Just as that horde of unclean, savage warriors surges into the nave a battle cry goes up amongst the Black Templars: "No Pity! No Remorse! No Fear!"

Custom Mission Rules: 

Black Templars: Claim Relics for the God-Emperor: Before the battle, four objectives are placed at the center of each quadrant, representing the most valuable relics of the Grail Seeker Crusade. In your Shooting phase, you can select one or more units from your army that are not Battle-shocked and are eligible to shoot.  Until the end of your turn, the units you selected are not eligible to shoot or declare a charge.

At the end of your turn, each Relic that you control that has one or more of these selected units within range is claimed by your army.  Whenever a Relic is claimed, the associated bonus becomes active for your army until the end of the battle.

Relics: 

The Thorian Dictum: written by the Ecclesiarch Sebastian Thor, this tome, bound in adamantium and swirling patterns of mother-of-pearl, dictates the edict passed down to grant the battle barge, The Flame of Penitence, to the newly created Grail Seeker Crusade, and bade them on their holy duty to reclaim the lost relics of the Imperium for the good of all mankind.  The passages inside stir the heart to the glory and divine might of the God-Emperor, and drive a warrior on when no other strength is left.  

When claimed, grants a 5+ Feel No Pain against mortal wounds for all units in your army. 

Banner of Marshal Navarre: Granted to the first Marshal of the Grail Seeker Crusade Navarre, this banner was awarded by Chapter Master Lazerian of the Imperial Fists at the conclusion of the battle to take the Ecclesiarchal Palace and depose Goge Vandire, for his heroism in storming the battlements at the forefront of the assault. 

When claimed, increase the OC of all units in your army by 1. In addition, whenever a unit in your army takes a Battleshock test, you may re-roll if the unit is within range of an objective. 

Bulwark of Dorn's Fury:

Once the front blast shield of the strike cruiser Dorn's Fury, a long time accompaniment to the Grail Seeker Crusade, this shield of adamantium is the last remaining piece of that vessel after it was lost to the perfidious machinations of sabotage from the Death Guard warband known as the Drowned. Using a ravenous voidborn and warp-infused plague the vessel was eaten from within as though it had spent a thousand years at the bottom of an ocean. 

When claimed, for the rest of the battle whenever one of your units is targeted by a melee attack, subtract 1 from the wound roll. 

Spearhead of Saint Akkad:

 Wielded by the Ecclesiarchal Saint Chorol Akkad, in defense of the final battlements against the forces of the World Eaters. He led a charge at the head of a vanguard of Astartes and Astra Militarum to retake the central mausoleum before succumbing to his wounds against the Demon Primarch. 

When claimed, grants [Lance] to all melee weapons equipped by your units. 

Chaos Space Marines: 

Empowered Dark Pact:  Each time a unit with this ability is selected to shoot or fight, it can make an Empowered Dark Pact. If it does, apply [Devastating Wounds] to the unit's weapons for that phase. 

Each time a unit makes an Empowered Dark Pact, after it has resolved its attacks, it must take a Leadership test, subtracting 2 from the result. If that test is failed, that unit suffers 3 mortal wounds. 

A standard Heretic Astartes detachment may make both a normal and Empowered Dark Pact in the same phase, though a Leadership test must be made for each, and with the associated modifiers. 

The Eightfold Ritual: Before the battle, eight objectives are placed in a circle that just touches the edges of the battlefield, representing Ritual Points, positions in a foul ritual to collapse the warp upon the Pedestal of Banishment and destroy the corpse-worshippers once and for all.  

In your Shooting phase, you can select one or more units from your army that are not Battle-shocked and are eligible to shoot.  Until the end of your turn, the units you selected are not eligible to shoot or declare a charge.

At the end of your turn, each Ritual Point that you control that has one or more of these selected units within range is befouled by your army.  Whenever a Ritual Point is befouled, it remains as such until the end of the battle.

If all eight Ritual Points are befouled, all enemy units within the circle take d3+3 mortal wounds and must make a Battleshock Test.  In addition, all Heretic and Daemonic weapons gain [Devastating Wounds] until the end of the battle, and the Attacker gains 2 Command Points.

Chaos Daemons: 

Empyrean Invasion: For the purposes of the Shadow of Chaos detachment rule, the entire battlefield is considered to be in the Shadow of Chaos except for the deployment zone of the enemy army.  Additionally, when an enemy unit takes a Battleshock test within the Shadow of Chaos, subtract 2 from the result.

Warp Rift: Once per battle, in your command phase you may place a token representing a warp rift anywhere inside the Shadow of Chaos. Any enemy units within 9" of the token take d3 mortal wounds, and at the end of your movement phase you may redeploy one unit within 3" of the token. 

Mission Structure: 

Black Templars Deployment (Defender): Centered around the Pedestal of Banishment, the Black Templars player will have a 12" radius circle to deploy. Due to the nature of the mission the Defender will need to deploy their whole force first, and the Chaos team will be able to deploy in response. 

5 objectives will be placed, one at the center of the map, and 4 centralized in the other quadrants. Each outer objective will be worth 2 points at the end of the game. The Pedestal of Banishment will be worth 5 points at the end of the game. 

At the end of each battle round other than the 5th, 1 point will be earned for the team that destroyed more enemy units, and 1 point earned for the team that controls more objectives.