In version 3 of the GNU General Public License (GPLv3), the term "the Program" means one particular work that is licensed under GPLv3 and is received by a particular licensee from an upstream licensor or distributor. The Program is the particular work of software that you received in a given instance of GPLv3 licensing, as you received it.

"The Program" cannot mean "all the works ever licensed under GPLv3"; that interpretation makes no sense, because "the Program" is singular: those many different programs do not constitute one program.

In particular, this applies to the clause in section 10, paragraph 3 of GPLv3 which states

[Y]ou may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.

This is a condition that limits the ability of a GPLv3 licensee to bring a lawsuit accusing the particular GPLv3-covered software received by the licensee of patent infringement. It does not speak to the situation in which a party who is a licensee of GPLv3-covered program A, but not of unrelated GPLv3-covered program B, initiates litigation accusing program B of patent infringement. If the party is a licensee of both A and B, that party would potentially lose rights to B, but not to A.

Since software patents pose an unjust threat to all software developers, all software distributors, and all software users, we would abolish them if we could. Indeed, we campaign to do so. But we think it would have been self-defeating to make the license conditions for any one GPL-covered program go so far as to require a promise to never attack any GPL-covered program.