I'm also not understanding your question, but note that the correct equation is ##E=m c^2 \gamma##, where ##\gamma=1/\sqrt{1-v^2/c^2}## is the same Lorentz factor that also enters the time-dilation formula. Indeed if a clock shows ##\Delta t## in its rest frame an observer moving with velocity ##v## relative to the clock will measure ##\Delta t'=\gamma \Delta t##.
The similarity between the equation for energy and the time dilation formula is not a surprise, because it's closely connected. One defines everything in relativity in covariant quantities. Thus having vectors like the time-position four-vector in special relativity and wants to define covariant quantities by time derivatives one uses proper time ##\mathrm{d} \tau = \sqrt{1-v^2/c^2} \mathrm{d} t##, because that's a scalar under Lorentz transformations and thus
$$V^{\mu}=\mathrm{d}_{\tau} x^{\mu}$$
is a four-vector, the four-velocity of the particle. In terms of usual velocity (which is NOT a relativistically covariant quantity) this reads
$$(V^{\mu})=\begin{pmatrix} c \mathrm{d}_{\tau} t \\ \mathrm{d}_{\tau} \vec{x} \end{pmatrix},$$
but ##\mathrm{d}_{\tau} = \mathrm{d} t (\mathrm{d}_{\tau} t)=\gamma \mathrm{d} t##. Thus you get
$$V^{\mu}=\begin{pmatrix} \gamma c\\ \gamma \vec{v} \end{pmatrix},$$
where ##\vec{v}=\mathrm{d}_t \vec{x}## is the usual three-velocity measured in the lab frame.
Now four-momentum is defined as
$$p^{\mu} = m V^{\mu},$$
where ##m## is the invariant mass. To understand what the time-component means we note that
$$p^0=m c \gamma =m c \left (1+\frac{1}{2} \frac{v^2}{c^2} +\mathcal{O}(v^4/c^4) \right),$$
and this suggests to define ##p^0=E/c## with ##E## the energy of the particle, because for the reason that ##p^{\mu}## is a four-vector it's convenient to include the rest energy ##E_0=mc^2## in the energy of the particle, and then in the non-relativistic limit ##E=E_0 + mv^2/2##, and ##m v^2/2=E_{\text{kin}}## in Newtonian mechanics, where ##E_0## is simply an additive constant which is not changed in any way by any physical phenomenon.
Note that this is different in relativistic physics! The rest mass of a composite object is related to the energy of this object in its rest frame by ##E_0=m c^2##. E.g., if you have some macroscopic body its invariant mass changes with temperature, because if the body gets hotter the heat-energy gain ##\Delta Q## adds to the rest energy, i.e., the invariant mass of the body changes by the amount ##\Delta m=\Delta Q/c^2##.
Thus, while the invariant mass does not change by any physical processes within Newtonian mechanics (except you add or take away some matter to a composite object of course), relativity shows that this is only approximately right. In other words: The invariant mass is not a conserved quantity for a closed system in relativistic physics. Here only the energy of a closed system is conserved but not invariant mass!