Hi, Thanks for playing the game. You ran into the only bugs unfortunately which I did not have time to fix.
There are two known bugs which will be fixed with a patch, it is unfortunate that you ran into both of them.
1. Watch full story causes the levels not to work unless you restart. (this was a bit tricky to fix and identify honestly, I put the story mode for personal debugging and left it there :P)
2. In tutorial, if you kill the phantom before it disables the towers then the tutorial is stuck. (I initially put the fix in the build but later realised the code was overriding the behaviour. This is now fixed and in the next patch, which I would like you to play once I push it you can see it fixed.)
I have fixed both of them and am planning to push a bigger patch with the final level implemented, so I will ask you to wait on those bugs unfortunately.
The reason the towers would deactivate are as follows:
1. The phantom deactivates the towers it passes by.
2. The towers themselves deal damage to each other if they hit each other leading to them being disabled.
3. If you place the tower close to the Purple (static) rift then it periodically emits a wave which disables the towers.
There is also the blue (nexus) rift which emits nexus wave which kills the phantom and enables any deactivated towers.
Thank you for playing the game and leaving a feedback, its a shame you encountered all the few handful known bugs which I could not fix because of the time limit of the jam.