The Atheon boss is the final part of the Vault of Glass, following Gatekeepers and Relics. Congratulations! Initially this final battle is the toughest in the Raid, requiring the most intense coordination, but there are several strategies that will make it much easier.
If you've been carrying weaker players through the Raid so far, though, Atheon will highlight those deficiencies, so watch out.
How to kill Atheon, Time's Conflux
As well as being annoyingly tough, Atheon has a gimmick that sows chaos: at several points in the fight, he randomly teleports three of your fireteam to either Mars or Venus, effectively splitting you into a 'home' team and an 'away' team. In order to survive the fight and finish the Raid, you will need to learn the rhythms of both roles off by heart and communicate clearly with your comrades.
Before you begin, decide who is good with the Relic. You need to make sure at least four people on your team are confident with it, because that way you will always have a good Relic holder on the away team.
Away team: As soon as you are teleported, tell the home team where you are. "Mars left!" "Venus right!" You can't get much clearer than that.
Whether you're in Mars or Venus, you will spawn at the top of the stairs and on top of the Relic, so someone needs to pick it up. You are all marked for negation immediately, so your vision starts to go black.
If you are in Mars, there are three Hobgoblins at the bottom of the stairs. Let the Relic holder deal with them (shooting them will activate their shields, holding you up). To avoid their devastating sniper fire, the Relic holder should go around the pillar on the right and head down the stairs, then kill them quickly with heavy melee attacks. Once they are dead, go up the stairs and cleanse the others.
If you're in Venus, there is a Praetorian alongside two Goblins at the foot of the stairs. Everyone should immediately throw grenades in their direction to soften them up. The Relic holder should then descend to finish them off. Prioritise the Praetorian. As with Mars, make sure to go up the stairs after to cleanse the others.
Wherever you are, while the Relic holder is busy, the other two players should stay still initially. You are going to be dealing with the Oracles that will spawn in a daisy chain leading you back to the time gate. The first appears directly above you. Then they are evenly spaced all the way to the gate. You two need to stay tightly together so the Relic holder can cleanse you efficiently. Remember the cleanse ability requires charging first, so don't get impatient. Shoot Oracles while moving slowly but steadily forwards, together.
As soon as the away team destroys the last Oracle, Time's Vengeance comes into effect. Time's Vengeance lasts 30 seconds and massively amplifies any damage inflicted on Atheon, so it is absolutely key to finishing the fight.
In order to make the best use of Time's Vengeance, the away team should discipline themselves to shoot the last Oracle only as they reach the threshold of the time gate platform. That way they can duck through the gate with 25-30 seconds of Time's Vengeance still active, rather than 20 or less. Elongating the damage inflicted on Atheon with Time's Vengeance active will mean fewer teleportations and therefore less opportunity for mishap.
Home team: As soon as the others are teleported and identify their location, your role is simple: get your backside to that sync plate and hold it at all costs. You need to power up the time gate in order for the other team to return to your location and attack Atheon.
To complicate matters, Atheon summons an irritating Harpy variant known as Supplicants, who assault you in squads of three that alternate attacking left and right sync plates. They are not that tough, as it goes, but they do explode on death and will self-detonate if they get too close to you. The trick to avoiding this effect is to make sure you all stand on top of the pillar in the centre of the Vex sync plate. This significantly reduces the explosive impact.
Kill the Supplicants and don't be lazy when the away team starts to return - there is nothing worse than doing your job in Mars and Venus and then being killed by a Supplicant that your team-mates ought to have slain in your absence.
When Time's Vengeance is active: Once everyone is back through the gate, all six of you should quickly assemble in the centre of the arena, either on the platform suspended in midair or by the main door (agree which in advance) and begin firing upon Atheon.
The Relic holder must come to the side of whichever platform you're on that is closest to Atheon and hold the cleansing button down for as long as Time's Vengeance lasts. (Don't worry, the cleansing effect won't run out - it will keep cycling.) The cleansing bubble protects you from Atheon's attacks and also removes the negation mark from the away team, which has been activated again once you get back.
If you have a Titan Defender in your team, they should pop their Weapons of Light Super bubble just behind the Relic cleansing bubble and everyone should dip into it. This provides an additional damage-amplifying effect, which helps deal with Atheon even faster.
Now you just need to shoot him until Time's Vengeance runs out, then hide behind a pillar until three of you are teleported again. Then repeat. That's it.
There will be some tough times as you put all of this together. You can read it on the page a few times and feel you understand it, but it is only a guideline and there will be subtleties that you only figure out through experience. In other words, the above strategy is solid and will work, but given the amount of coordination and luck involved in getting everything to play out as you desire, you will probably wipe a few times before you pull it off.
Once you put it all together, though, you will be able to deal with Atheon in three or four away trips. Once he's dead, the Raid is done and you claim yet more loot.