I just played this combination and found it to be fantastic and would recommend it to anyone looking for a combo that can surprise other players extremely well.
For those that aren't already aware, Spies have some amazing special actions. "The Base is Not Enough" allows you to take control of an enemy minion of power 4 or less before a base breaks (sort of like Make Contact but with a level restriction) and "Live and Let Chum" lets you destroy an enemy minion of power 3 or less before a base breaks. The 4 power minion "Mole" lets you play an action as a special action before a base breaks as well. This can lead to some very interesting combinations since ninjas have a large number of actions that can be very effective in base breaking situations.
Looking at the Ninja deck, there's 3 Shinobis and a Hidden Ninja card. Between the two decks, that means you have 8 cards that allow you to have a special ability (mind you the Mole is only useful if you have an action card that you can use on the base). This allows for some insane power exchanges.
In a perfect world (I know it's not likely) where you had two Moles on a base already and an amazing hand, you could do the following
-Shinobi (+3 to you)
-Hidden Ninja the Ninja Master (+5 to you, -2 or higher to your enemy)
-The Base is Not Enough (+4 to you, -4 to enemy)
-Live and Let Chum (-3 to enemy)
-Mole ability with Poison (-4 or higher to enemy if they have actions)
-Mole ability with Seeing Stars (-3 to enemy)
This gives you a total of +12 power on a base and reduces your opponents by a minimum of -16. It would require 7 cards in your hand and two moles down already. I admit that this is overkill but it just goes to show the kind of power you have to change a situation on a base quickly.
Now probably the biggest downside to Ninjas has always been their inability to get through their deck. If Hidden Ninja, your Shinobis, Poison, or Ninja Master were at the bottom, you were bound to have a tough game. However, Spies have 10 different cards that let you pick up cards or move unwanted cards to the bottom of your deck. Because of this, it can be extremely easy to get at your 8 special cards while still picking up decent cards along the way. What I found to actually be the biggest hindrance is that I would often have too many specials in my hand that I didn't want to ditch but I couldn't play so I had to discard many half-decent cards along the way (mind you I played 1v1 which meant much slower base scoring).
I would strongly recommend trying out this combination. There is almost no way that you'll get screwed out of VP on a base since you often get the last word in with specials. Also, you dictate when you want a base or when you want to leave it but you'll always have your opponents second guessing their actions and putting more power than necessary down to secure their lead. While Ninjas with any other faction can mostly be countered merely by leading by 3 power on a base, there is no telling what will happen with Ninja/Spies
Marc Nelson Jr.
Of course Spies and Ninjas go together!
Yeah, Spies are nasty. My wife played them tonight - I needed to score a base to win, but with her holding a full hand I knew I needed to really pile it on to be sure. Sure enough, here come Base, Chum, and Mole!
I did pull out the win, but the threat really affects the way you play them.