If you want to finish The Dark Below's storyline, you need to complete the new strike - The Will of Crota.
Destiny: The Dark Below guide - The Will of Crota strike
Destiny: The Dark Below ties story, Patrol and now Strike content together into one questline. If you've done everything else, it's time to take down Ominigul.
This is the final mission of Eris's quest content, although there's still lots to do in The Dark Below outside the new story.
The Will of Crota is a level 26 strike. Launch it from the Earth section of your navigator; I can't guarantee it'll count towards quest progress if you use the level 26 Strike playlist.
The strike begins simply enough, kicking off with you and your teammates making your way towards and then through the Terrestrial Complex. You're after the Hive, but the Fallen are out in force. Ignore any enemies on your way until you reach the Darkness zone.
This is quite a difficult battle, taking place in the same arena as a challenging early story mission. You'll face much tougher enemies this time, but the same tactics apply - use choke points and retreat through an exit if things get too tough. The enemies tend to swarm you, so your new Murmur should come in handy.
Eventually the Hive will join in, but this is actually a help; the Fallen and Hive will fight each other, Group up at one end of the room and slowly advance, killing the majority of them off. Finally, the deadly lasers on the door will go down, allowing you to climb up to the area where you completed The Last Array.
This is a very linear battle, with little room for fancy footwork. The Fallen's assault is relentless, and it should be all your team can do to inch forward slowly. Don't get separated; stick together and take ground steadily.
About the time you approach the array itself you'll start seeing a greater influx of Captains, culminating in a Baron. Resist the urge to get up close to them; they have powerful melee attacks, like a Stealth Vandal.
When the Baron goes down, proceed through the complex to Skywatch, and then down the tunnel under the Hive Seeder to the Jovian Complex, a new area.
You'll need to deploy a Ghost at the door, after which you'll pass through and very shortly see Omnigul. Pour a bit of lead into her and she'll vanish. You'll then have another very linear fight, creeping forward around the corner and uphill through massive resistance until you reach the final room.
Things begin to get uncomfortable now, but the first half of the battle with Omnigul isn't too bad, and she tends to stick to one position. If you split your party so that two of you head up on the catwalks, staying behind cover and taking turns to take pot shots at Omnigul, the other can stay at ground level near the entrance to the area, keeping her in a cross fire zone, and ensuring she never has a chance to refill her shields.
When Omnigul's health gets low, though, it goes bananas. She begins spawning in huge numbers of melee Knights as well as Acolytes and Thralls. You want your fireteam to be watching each other's backs; maybe get your best DPS chipping away at Omnigul with the other two protect them. Chaining supers is deadly effective in these close quarters, especially if you have Warlocks and Titans.
When you have defeated Omnigul, return to Eris to collect your prize - a Legendary class item.