The bloons are a species of Eldritch Abominations.In BTD 5 one map has the bloons come from somewhere other than offscreen- it has them come from an active volcano! Also, in Bloons Supermonkey the eponymous hero travels from plains to jungle to the Arctic to Hell to space. My assumptions is that the Supermonkey was going to the Bloons' home world through a portal of sorts. This portal, with one end at an active volcano at the North/South pole of the Monkey's world, goes through Hell (which likely gives quicker transport like the Nether in Minecraft). Another map in BTD 5 has you defend the solar system from the bloon menace. These bloons can go through lava and survive the void of space.
The bloons are possibly radioactiveThink about it, the material you use to produce bloons for Pv P in monkey city is called bloontonium. This could also explain why they hurt whatever point the monkeys are defending offscreen, and why higher ranked bloons do more damage (higher concentration of bloontonium.)
Bloons and Monkeys are how wars are fought in the futureHow else to explain why the monkeys defending pull out the stops for overkill when fighting balloons.
- This also explains why there is a new "ultimate" bloons in the sequels; the side attacking knows that their strongest bloons aren't cutting it.