No cartilage between big toe and foot. all of the pain is in my arch. dr. is recommending fusion . will i be able to run? alternatives to fusion?

Do your homework.: Fusion is one possibility but, depending on the circumstances, there could be others. There are a lot of things to consider and your activity level is certainly an important one. Consider a second opinion or maybe even a couple more opinions. Implants or fake joints (spacers) seem to work well in the short term but most fail in time, especially with excessive activity.