Aragorn is enough of a Runner that he wouldn't have been working for a wimp like Gunderson- OTOH, he's not in Caleb's league, either.
Check with Mortimer Reed- he'll fill you in. Seems that Aragorn went on a solo run against Mitsuhama, and got caught. He's still in their offices, awaiting interrogation. Run time...

In the Penumbra District at the north side, you'll find Mitsuhama's offices where Aragorn is being held.
I don't think I need to tell you how to pull off an Extraction Run by now, do I? The only difference here, is that Aragorn doesn't need to be escorted out personally- he can make his own escape once you make a path for him by reaching his location (he's on the fifth floor, take the elevator to the right).
Return back to Owlfeather and he'll repay you with the name of Spirit Eyes.

At the Medicine Lodge on Council Island, a request to speak with the most wise one will get you a pass to Spirit Eyes. He can help you- if you help him. He'll need three ingredients for the ritual to discover the identity of your brother's murderer.

The first is a Gargoyle's horn. You can find one in any location where ghouls also hang out- I prefer the Redmond Barrens and the building in the northeast corner.

The next ingredient is a hell hound's skin. You can get them in the Sinsearach- so jump over to the walkthrough for Frosty if you haven't already, and we can pick one up along the way. Failing that, you can always go back to Renraku- sometimes they assault you with patrols of hell hounds.

Last one- the hardest. Find the living scale of a feathered serpent. Back to the Salish-Sidhe.

Past the village, through the southeast cave exit. South, then take the west fork in the road, into another cave. South, West, South, to the area where the Sinsearach may be found. Take the southeast cave entrance, then south, then west, then west, another west and then...
BOSS BATTLE! Save before taking the third western exit (even though it's a cave, it counts as being outdoors for the purposes of saving, then expect to do battle with a Renraku Strike Team. These guys are tough, but you should be tougher (indeed, the Hellhounds and Wendigos you've been facing in the Salish-Sidhe were as tough as these guys). Hit fast, hit first, and they won't have a chance to perforate you with high caliber rounds. The next western exit is the biggie.

And I do mean BIG. A feathered serpent- a Latin-American dragon, facing off against Renraku. You quickly finish off the humans, then face the dragon. Speak the truth and be rewarded. Licourtrix will reward your honest answer by bonding himself to you as your lifelong protector, then gives you a scale as he leaves. Back to Council Island.

Spirit Eyes performs the ritual as agreed upon, summoning forth the face of Thon. A jackal headed demonic being, he is your brother's killer, and a great instrument of evil in the world. But at any rate, this quest segment is done. Go see Frosty in the Sinsearch, do her quests if you haven't already, and we find ourselves nearing the end.

Harlequin and the Final Battle