Tip: farm the first boss, but kill him before you get $1600 or 1700 (assuming you didn't miss too many previous kills). Otherwise, he flies off the screen, never to be seen again, and you're forced to restart.
How to beat Vandheer (hard mode):
STAGE 1: He walks, occasionally using specials. Bait his combo, jump over, turn around, and A-combo from behind.
STAGE 2: He runs, using skills more frequently. Same as Stage 1, but harder.
STAGE 3: He constantly spams D and W. The only time you can hit him is right after his D attack. You must time your A-combo to land a hit after his invincibility ends, but before he blinks away for another D or W.
TIPS: Never be approach from his front - always jump over him. Stay away from the edges, leading him back to the middle. Dodge his D by walking to the right slowly. Dodge S by running away while A-comboing. Patience. Building up your special bar isn't worth getting hit. Don't use S skill against him.
ADVANCED TIPS: When baiting him, tap the "back" direction before jumping over so you're facing him when you land. Always use your full A-combo, except before falling off the edge. If you stop/he retaliates, you probably did something wrong.
I'm gonna have to criticize on how this game's implemented/performance. I've never coded flash, so perhaps it's a limitation you can't control. It seems like the longer the blue/red tape sequence, the longer the delay between loops. To me, this implies that you're recopying the data structure over and over again in order to append a different color to the end of it. If that's the case, I suggest using a circular list, or implement a circular list using an array with a moving head/tail. It'll improve the performance of the game quite a bit.
Are people seriously having that much trouble with ninjas and assassins?
Ninjas: Temple near front, to make them burn their stealth. Use fast-reload, instant-hitting towers to finish them off where they de-stealth. Later on, esp. if on top of a tower, level as much as possible as a burning temple . It can easily one-shot ninjas and splash even when stealthed. If you can't use a temple, just do the same thing with den->ballista den.
Assassins: More towers. Numerous, multiple attacks work best (i.e. crypts, esp. /w fear+freeze). Same for boss assassins.
Boss Ninjas: Upgrade the meteor spell and mana pool. Multi-cast by holding down shift. Lucky fear/freeze/burn helps too.
If you still can't kill them off fast enough, just grind some experience/skills.
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