Assuming this is do-able, you'd be able to do this for both main bases because they'd be seperate objects. For instance, the East Base would have control over a bubble at the Axis base, and one at the Allies base. When the Allies cap the flag, the bubble on the Axis base disappears (but the bubbles spawned by the other two flags would still be active), and the bubble over the Allies base would remain because the Axis don't have control of the point.
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