By the time of the Phyrexian War, Wes was a General, and had been given command of all military forces on Taanab. He and his forces fought valiantly at Taanab, but eventually the planet was captured. Wes and the Wraiths started an insurgency movement against the Phyrexian occupation force, to keep the enemy distracted long enough for the Galactic Alliance to send aid. However, when that aid came, Wes stayed behind to keep the enemy's attention on him and cover the Wraiths' escape. Once the Wraiths were safely out, Wes set off a chain of explosions that destroyed nearly the entire Phyrexian force on Taanab, but also killed him.
Behind the scenesEdit
I have often had to explain and/or defend my choice to kill Wes off. The simple truth of the matter is, age killed him long before I decided to make his death a physical one. The eternally youthful comic relief character had finally started to get serious... in Wes Janson's case, not a good thing.
Wes is a canon character, so look here if you want canonical information.