Seek Harlequin in the Puyallup Barrens' Tarlisar Garden Apartments. He'll fill you in on the whole story about Thon, Vigore and Jarl, and Renraku. Then he assigns you to find out about Vigore and Jarl.
To find them- of all the people, Gunderson, the wimpiest of all Johnsons, is the man to see. He'll send you to their secret base in the Rat's Nest, right there in the Redmond Barrens. You won't find them, but you WILL find the map! Go back to Harlequin and prepare for the final confrontation.

Final Confrontation: Harlequin will give you one last chance to prepare- assemble your most combat worthy Runners, your biggest guns, your most powerful spells, your heaviest armor (I highly recommend you get 3 suits of Heavy Combat Armor from the Yakuza contact), your medkits and spell focuses and all the rest.

When you go into the tomb, you go in blasting. The toughest foes you have yet faced await you- concentrate your heavy firepower on them, and they'll go down, but hit fast and hit first. Through the door to the north...

FINAL BOSS BATTLE: Thon is... too powerful. You can't kill him (or shouldn't, anyway- see Secrets). Instead, he forces you to kneel with his awesome might. But then the Council uses THEIR powers to weaken him, making him susceptible to physical damage. Take out Vigore and Jarl, then focus on Thon (making sure to heal up anyone who gets taken out), with the understanding that he heals as rapidly as you damage.

But you don't NEED to kill him- just hold out long enough for Licourtrix to show up and give him a taste of dragonish morning breath. With Licourtrix's aid, you will finish off Thon.

Sit back and enjoy the ending. Well done, Shadowrunner!