555 Astable Multivibrator Voltage Spikes
I think the "spikes" are there because that's where the 555's output voltage is supposed to be, but something's pulling it down.

If you've got a 7805 running the 555 and [555] pin 3 drops down to 2V, then - assuming a good 555 and 7805 - either the 7805's input is dropping below the 7805's regulating threshold or the TIP31's base resistor's resistance is way too small.

If you're using your 12V supply as the input to the 7805 and the load pulls it down enough, that could be the problem. 

The first thing I'd do, though, would be to check the base resistor and make sure it's not too small.

If it isn't, the next thing I'd do would be to put my scope across the 7805's input in order to rule that out, and if it's not the problem I'd still connect a BFC across the 7805's input and 100nF directly across 555 pins 1 and 8.  The BFC, just because, and the 100nF because the 555 has horrible shoot-through when it switches. If it is the problem, then a stiffer 12V supply is probably the solution.